3CIF
Crystal Structure of C153S mutant glyceraldehyde 3-phosphate dehydrogenase from Cryptosporidium parvum
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3CHZ | PDB ENTRY 3CHZ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.5 | 298 | 20% PEG 3000 Prior to crystallization, the protein was incubated with 2 mM NAD and 11 mM D-L-glyceraldehyde 3-phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.50 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.19 | 43.82 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 68 | α = 90 |
b = 120.1 | β = 92.08 |
c = 79.28 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 103 | CCD | MAR225 | 2005-06-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | APS | 22-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
1 | 2 | 20 | 99.7 | 0.087 | 11.9 | 7.1 | 84846 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2 | 2.07 | 99.3 | 0.309 | 6.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 3CHZ | 2 | 20 | 79294 | 4253 | 98.5 | 0.17921 | 0.17756 | 0.20973 | RANDOM | 21.914 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.24 | 0.28 | 0.6 | -0.34 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.914 |
r_dihedral_angle_4_deg | 18.98 |
r_dihedral_angle_3_deg | 12.228 |
r_dihedral_angle_1_deg | 4.937 |
r_scangle_it | 1.102 |
r_angle_refined_deg | 0.979 |
r_scbond_it | 0.679 |
r_mcangle_it | 0.625 |
r_mcbond_it | 0.354 |
r_nbtor_refined | 0.297 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10072 |
Nucleic Acid Atoms | |
Solvent Atoms | 723 |
Heterogen Atoms | 230 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
CNS | phasing |
CNS | refinement |