1O62

Crystal structure of the apo form of a PLP-dependent enzyme


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1hanging drop vapor diffusion7.5285pH 7.5, hanging drop vapor diffusion, temperature 285K
Crystal Properties
Matthews coefficientSolvent content
2.8857.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 152.189α = 90
b = 152.189β = 90
c = 77.119γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayIMAGE PLATERIGAKU RAXIS IVSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODE1.54

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
12.15098.30.0649.72.55842158421
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)
12.12.2198.30.2663.32

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT2.149.825842159500.2240.25527.602
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]
-0.569-0.284-0.5690.853
RMS Deviations
KeyRefinement Restraint Deviation
p_scangle_it2.494
p_mcangle_it1.762
p_scbond_it1.694
p_angle_d1.413
p_planar_tor1.399
p_mcbond_it1.012
p_chiral_restr0.102
p_bond_d0.006
p_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5860
Nucleic Acid Atoms
Solvent Atoms412
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
TRUNCATEdata scaling