2VD9

The crystal structure of alanine racemase from Bacillus anthracis (BA0252) with bound L-Ala-P


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VD8PDB ENTRY 2VD8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.525% (W/V) POLYETHYLENE GLYCOL 3350, 0.1M BIS-TRIS PH6.5, SOAKED IN 10MM L-ALA-P FOR 45 MINUTES, CRYOPROTECTED IN 25% GLYCEROL
Crystal Properties
Matthews coefficientSolvent content
2.2846

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.692α = 90
b = 96.504β = 90
c = 140.66γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2007-03-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
12.15099.90.237.16.948124
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)
12.12.1890.881.24.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2VD82.145.6445596243499.70.190.1880.239RANDOM14.3
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]
0.03-0.050.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.064
r_dihedral_angle_4_deg12.771
r_dihedral_angle_3_deg11.569
r_dihedral_angle_1_deg6.288
r_angle_refined_deg1.195
r_mcangle_it0.914
r_angle_other_deg0.912
r_scangle_it0.859
r_mcbond_it0.769
r_scbond_it0.535
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.064
r_dihedral_angle_4_deg12.771
r_dihedral_angle_3_deg11.569
r_dihedral_angle_1_deg6.288
r_angle_refined_deg1.195
r_mcangle_it0.914
r_angle_other_deg0.912
r_scangle_it0.859
r_mcbond_it0.769
r_scbond_it0.535
r_symmetry_vdw_other0.231
r_symmetry_vdw_refined0.224
r_nbd_other0.195
r_symmetry_hbond_refined0.193
r_nbd_refined0.189
r_nbtor_refined0.175
r_xyhbond_nbd_refined0.153
r_nbtor_other0.084
r_chiral_restr0.068
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6196
Nucleic Acid Atoms
Solvent Atoms871
Heterogen Atoms94

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing