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Alanine Racemase from Streptomyces coelicolor A3(2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VFH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.1 M BIS-TRIS propane pH 8.5, 0.2 M NaBr, 20% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.12 42.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.96 α = 90 b = 87.17 β = 102.26 c = 109.626 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2015-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.972422 ESRF ID23-1
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 2.8 47.78 95.96 0.249 3.8 3.4 32860
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.94 84.1 1.3
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 1VFH 2.8 47.78 32860 1693 95.96 0.211 0.20847 0.2132 0.25918 0.2612 RANDOM 44.888
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] -1.3 -1 5.96 -3.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.51 r_dihedral_angle_4_deg 17.845 r_dihedral_angle_3_deg 15.6 r_long_range_B_other 8.398 r_long_range_B_refined 8.397 r_dihedral_angle_1_deg 6.423 r_scangle_other 5.38 r_mcangle_it 4.971 r_mcangle_other 4.971 r_scbond_it 3.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.51 r_dihedral_angle_4_deg 17.845 r_dihedral_angle_3_deg 15.6 r_long_range_B_other 8.398 r_long_range_B_refined 8.397 r_dihedral_angle_1_deg 6.423 r_scangle_other 5.38 r_mcangle_it 4.971 r_mcangle_other 4.971 r_scbond_it 3.29 r_scbond_other 3.29 r_mcbond_it 3.081 r_mcbond_other 3.081 r_angle_refined_deg 1.601 r_angle_other_deg 1.393 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.005 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11337 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing