4R68
Lactate Dehydrogenase in complex with inhibitor compound 31
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4M49 | PDB ENTRY 4M49 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.2 | 293 | PEG 3350, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.18 | 43.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 77.642 | α = 90 |
b = 81.07 | β = 98.75 |
c = 102.476 | 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 | 110 | PIXEL | DECTRIS PILATUS 6M | 2012-04-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.97945 | SSRL | BL11-1 |
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 | 2.11 | 57.124 | 96.8 | 0.098 | 10.3 | 3.4 | 70298 | 70252 | 1.33 | -3 | 22.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | PDB ENTRY 4M49 | 2.112 | 57.124 | 1.33 | 70298 | 70252 | 1425 | 97.23 | 0.157 | 0.1561 | 0.1553 | 0.1967 | random |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 19.086 |
f_angle_d | 1.094 |
f_chiral_restr | 0.071 |
f_bond_d | 0.007 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10204 |
Nucleic Acid Atoms | |
Solvent Atoms | 937 |
Heterogen Atoms | 385 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
PHASER | phasing |
PHENIX | refinement |
XDS | data reduction |
SCALA | data scaling |