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Crystal structure of a mandelate racemase/muconate lactonizing enzyme-like protein from Rubrobacter xylanophilus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 294 100mM Bis-Tris pH 6.5, 1.4M Ammonium phosphate, VAPOR DIFFUSION, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3.3 62.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 193.1 α = 90 b = 193.1 β = 90 c = 113.483 γ = 90
Symmetry Space Group P 43 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 2008-04-11 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 2.3 48.28 98.4 0.16 0.16 8.5 10.4 93498 93498 34.7
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 2.3 2.42 98.3 0.431 0.431 3.5 10.3 13481
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 2.3 20 93295 93295 4684 98.2 0.245 0.243 0.2519 0.292 0.2998 RANDOM 43.459
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] -0.06 -0.06 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.975 r_dihedral_angle_4_deg 17.034 r_dihedral_angle_3_deg 15.084 r_dihedral_angle_1_deg 6.215 r_scangle_it 4.9 r_scbond_it 3.037 r_mcangle_it 1.685 r_angle_refined_deg 1.676 r_mcbond_it 0.89 r_chiral_restr 0.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.975 r_dihedral_angle_4_deg 17.034 r_dihedral_angle_3_deg 15.084 r_dihedral_angle_1_deg 6.215 r_scangle_it 4.9 r_scbond_it 3.037 r_mcangle_it 1.685 r_angle_refined_deg 1.676 r_mcbond_it 0.89 r_chiral_restr 0.105 r_bond_refined_d 0.019 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10768 Nucleic Acid Atoms Solvent Atoms 512 Heterogen Atoms 14
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction SHELXCD phasing SHELXE model building