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Crystal structure of the CBS pair of possible D-arabinose 5-phosphate isomerase yrbH from Escherichia coli CFT073
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 291 0.1M CHES pH 9.5, 20% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.13 42.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.109 α = 90 b = 108.458 β = 90 c = 104.849 γ = 90
Symmetry Space Group C 2 2 21
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 CUSTOM-MADE 2008-12-13 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97937, 0.97923 APS 19-BM
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 2.03 50 99.2 0.093 45.14 9.6 18777 18777 -3 45.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.03 2.07 99.8 0.587 9.3 946
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 (All) 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 MAD THROUGHOUT 2.1 50 16930 16930 863 99.08 0.213 0.213 0.211 0.2568 0.243 0.2763 RANDOM 37.11
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] -2.22 -0.15 2.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.618 r_dihedral_angle_4_deg 18.125 r_dihedral_angle_3_deg 16.355 r_dihedral_angle_1_deg 6.597 r_scangle_it 3.776 r_scbond_it 2.363 r_angle_refined_deg 1.562 r_mcangle_it 1.531 r_angle_other_deg 0.874 r_mcbond_it 0.817
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.618 r_dihedral_angle_4_deg 18.125 r_dihedral_angle_3_deg 16.355 r_dihedral_angle_1_deg 6.597 r_scangle_it 3.776 r_scbond_it 2.363 r_angle_refined_deg 1.562 r_mcangle_it 1.531 r_angle_other_deg 0.874 r_mcbond_it 0.817 r_mcbond_other 0.169 r_chiral_restr 0.076 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1860 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 36
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MLPHARE phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing SHELXD phasing SHELXE model building SOLVE phasing RESOLVE phasing ARP/wARP model building CCP4 phasing O model building Coot model building