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The crystal structure of alanine racemase from Bacillus anthracis (BA0252)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SFT PDB ENTRY 1SFT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 25% (W/V) POLYETHYLENE GLYCOL 3350, 0.1 M BIS-TRIS PH 6.5
Crystal Properties Matthews coefficient Solvent content 1.99 38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.552 α = 90 b = 88.365 β = 90 c = 138.968 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 1.47 50 96.3 0.11 18.6 9.9 116056
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 1.47 1.52 78.3 0.95 1.2 4.6
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 1SFT 1.47 44.19 110132 5826 96.2 0.169 0.168 0.1745 0.199 0.2063 RANDOM 10.33
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.263 r_dihedral_angle_4_deg 11.453 r_dihedral_angle_3_deg 10.772 r_dihedral_angle_1_deg 6.257 r_scangle_it 3.038 r_mcangle_it 2.201 r_scbond_it 1.987 r_mcbond_it 1.826 r_angle_refined_deg 1.412 r_angle_other_deg 1.024
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.263 r_dihedral_angle_4_deg 11.453 r_dihedral_angle_3_deg 10.772 r_dihedral_angle_1_deg 6.257 r_scangle_it 3.038 r_mcangle_it 2.201 r_scbond_it 1.987 r_mcbond_it 1.826 r_angle_refined_deg 1.412 r_angle_other_deg 1.024 r_symmetry_vdw_refined 0.238 r_chiral_restr 0.219 r_symmetry_vdw_other 0.217 r_nbd_refined 0.215 r_nbd_other 0.202 r_nbtor_refined 0.181 r_symmetry_hbond_refined 0.165 r_xyhbond_nbd_refined 0.151 r_nbtor_other 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 6205 Nucleic Acid Atoms Solvent Atoms 1020 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing