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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 8.5 298 lithium sulfate, PEG 4000, pH 8.5, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.5 50.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.669 α = 90 b = 116.669 β = 90 c = 120.616 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 IV 2003-08-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 98.8 0.096 8.3 773477 71855
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 98.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 773477 67232 3584 98.82 0.17605 0.17605 0.17273 0.23835 RANDOM 31.349
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] 0.91 0.91 -1.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.264 r_scangle_it 1.807 r_mcangle_it 1.779 r_angle_refined_deg 1.328 r_scbond_it 1.056 r_mcbond_it 1.054 r_angle_other_deg 0.736 r_symmetry_vdw_other 0.286 r_symmetry_hbond_refined 0.264 r_nbd_other 0.258
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.264 r_scangle_it 1.807 r_mcangle_it 1.779 r_angle_refined_deg 1.328 r_scbond_it 1.056 r_mcbond_it 1.054 r_angle_other_deg 0.736 r_symmetry_vdw_other 0.286 r_symmetry_hbond_refined 0.264 r_nbd_other 0.258 r_xyhbond_nbd_refined 0.242 r_nbd_refined 0.219 r_symmetry_vdw_refined 0.115 r_nbtor_other 0.089 r_chiral_restr 0.073 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11064 Nucleic Acid Atoms Solvent Atoms 700 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing