1Y7M | pdb_00001y7m

Crystal Structure of the B. subtilis YkuD protein at 2 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.9294.1PEG 3350, acetate, lithium sulfate, cadmium chloride, pH 4.9, VAPOR DIFFUSION, SITTING DROP, temperature 294.1K, pH 4.90
Crystal Properties
Matthews coefficientSolvent content
2.448.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.276α = 90
b = 63.91β = 90
c = 93.679γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77.3CCDADSC QUANTUM 42004-04-04MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X9B0.97946, 0.97919, 0.97178NSLSX9B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.053099.10.05715.52.2218052
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.052.12990.4592.82.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT2.05302180520691111499.80.2140.2110.250.270.3RANDOM23.6
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
4.23-1.75-2.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.449
r_scangle_it2.9
r_scbond_it1.872
r_angle_refined_deg1.441
r_mcangle_it0.968
r_angle_other_deg0.854
r_mcbond_it0.548
r_nbd_other0.237
r_symmetry_vdw_other0.225
r_nbd_refined0.206
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2468
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing