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Crystal structure of a mandelate racemase/muconate lactonizing enzyme from Roseovarius sp. HTCC2601
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 294 100mM Tris-HCl pH 8.5, 25% PEG 3350, 200mM Magnesium chloride, VAPOR DIFFUSION, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.28 46.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.381 α = 90 b = 136.381 β = 90 c = 80.925 γ = 90
Symmetry Space Group P 4 21 2
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 MAR CCD 165 mm 2007-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97958 APS 31-ID
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 1.72 96.436 98.9 0.086 0.086 22.2 12 81085 81085 17.8
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 1.72 1.81 93 0.306 0.306 6.1 10.9 10981
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.72 20 81006 81006 4061 99.7 0.167 0.165 0.1758 0.191 0.2009 RANDOM 15.922
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] 0.02 0.02 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.606 r_dihedral_angle_4_deg 16.782 r_dihedral_angle_3_deg 11.735 r_dihedral_angle_1_deg 7.483 r_scangle_it 3.319 r_scbond_it 2.364 r_angle_refined_deg 1.341 r_mcangle_it 1.338 r_mcbond_it 1.154 r_angle_other_deg 0.902
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.606 r_dihedral_angle_4_deg 16.782 r_dihedral_angle_3_deg 11.735 r_dihedral_angle_1_deg 7.483 r_scangle_it 3.319 r_scbond_it 2.364 r_angle_refined_deg 1.341 r_mcangle_it 1.338 r_mcbond_it 1.154 r_angle_other_deg 0.902 r_symmetry_vdw_other 0.356 r_symmetry_vdw_refined 0.315 r_nbd_refined 0.222 r_mcbond_other 0.22 r_nbd_other 0.204 r_nbtor_refined 0.177 r_symmetry_hbond_refined 0.16 r_xyhbond_nbd_refined 0.144 r_nbtor_other 0.086 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5626 Nucleic Acid Atoms Solvent Atoms 687 Heterogen Atoms 5
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction CCP4 data scaling SHELXCD phasing SHELXD phasing SHELXE model building