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Structural Basis for Catalytic Racemization and Substrate Specificity of an N-Acylamino Acid Racemase Homologue from Deinococcus radiodurans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R0M PDB ENTRY 1R0M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 298 lithium sulfate, PEG 4000, pH 8.0, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.47 50.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.159 α = 90 b = 116.159 β = 90 c = 120.426 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 113 IMAGE PLATE RIGAKU RAXIS 2003-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL12B2 0.8 SPring-8 BL12B2
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 2.3 30 98.3 0.096 8.6 1416552 66037
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.38 99.2
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1R0M 2.3 30 66037 3511 98.29 0.17399 0.17121 0.22742 RANDOM 23.881
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] 0.49 0.49 -0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.449 r_scangle_it 1.694 r_mcangle_it 1.692 r_angle_refined_deg 1.321 r_mcbond_it 0.995 r_scbond_it 0.991 r_angle_other_deg 0.745 r_symmetry_vdw_other 0.268 r_nbd_other 0.262 r_symmetry_hbond_refined 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.449 r_scangle_it 1.694 r_mcangle_it 1.692 r_angle_refined_deg 1.321 r_mcbond_it 0.995 r_scbond_it 0.991 r_angle_other_deg 0.745 r_symmetry_vdw_other 0.268 r_nbd_other 0.262 r_symmetry_hbond_refined 0.23 r_nbd_refined 0.228 r_xyhbond_nbd_refined 0.215 r_nbtor_other 0.089 r_symmetry_vdw_refined 0.082 r_chiral_restr 0.076 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11236 Nucleic Acid Atoms Solvent Atoms 842 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing