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Crystal structure of a putative mandelate racemase/muconate lactonizing enzyme from Pseudovibrio sp.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SJN PDB ENTRY 3SJN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 30% PEG 8000, 100mM Imidazole/Hydrochloric acid pH 8.0, 200mM sodium chloride, Vapor diffusion, Sitting drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.38 48.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 201.793 α = 90 b = 117.313 β = 99.77 c = 143.127 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC QUANTUM 315r 2011-06-16 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.978 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 55.536 96 0.053 0.095 8.8 3.7 77549 77549
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.95 92.5 0.379 0.379 2 3.4 10798
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 (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 3SJN 2.8 39.41 75912 75912 3989 98.57 0.1971 0.1941 0.195 0.253 0.2548 RANDOM 85.245
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.813 r_dihedral_angle_4_deg 16.698 r_dihedral_angle_3_deg 14.909 r_dihedral_angle_1_deg 5.162 r_mcangle_it 4.554 r_mcbond_it 3.012 r_mcbond_other 3.012 r_angle_refined_deg 0.83 r_angle_other_deg 0.581 r_chiral_restr 0.052
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.813 r_dihedral_angle_4_deg 16.698 r_dihedral_angle_3_deg 14.909 r_dihedral_angle_1_deg 5.162 r_mcangle_it 4.554 r_mcbond_it 3.012 r_mcbond_other 3.012 r_angle_refined_deg 0.83 r_angle_other_deg 0.581 r_chiral_restr 0.052 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_gen_planes_other 0.001 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23530 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction CBASS data collection MOSFLM data reduction MOLREP phasing