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The crystal structure of alanine racemase from Bacillus anthracis (BA0252) with bound L-Ala-P
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VD8 PDB ENTRY 2VD8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 25% (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 coefficient Solvent content 2.28 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.692 α = 90 b = 96.504 β = 90 c = 140.66 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH 2007-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.1 50 99.9 0.23 7.1 6.9 48124
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.18 9 0.88 1.2 4.1
Refinement Statistics 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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2VD8 2.1 45.64 45596 2434 99.7 0.19 0.188 0.1908 0.239 0.2441 RANDOM 14.3
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 -0.05 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.064 r_dihedral_angle_4_deg 12.771 r_dihedral_angle_3_deg 11.569 r_dihedral_angle_1_deg 6.288 r_angle_refined_deg 1.195 r_mcangle_it 0.914 r_angle_other_deg 0.912 r_scangle_it 0.859 r_mcbond_it 0.769 r_scbond_it 0.535
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.064 r_dihedral_angle_4_deg 12.771 r_dihedral_angle_3_deg 11.569 r_dihedral_angle_1_deg 6.288 r_angle_refined_deg 1.195 r_mcangle_it 0.914 r_angle_other_deg 0.912 r_scangle_it 0.859 r_mcbond_it 0.769 r_scbond_it 0.535 r_symmetry_vdw_other 0.231 r_symmetry_vdw_refined 0.224 r_nbd_other 0.195 r_symmetry_hbond_refined 0.193 r_nbd_refined 0.189 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.153 r_nbtor_other 0.084 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 6196 Nucleic Acid Atoms Solvent Atoms 871 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing