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Phosphopentomutase from Bacillus cereus bound with ribose-5-phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3M8W PDB ENTRY 3M8W
Crystallization Crystal Properties Matthews coefficient Solvent content 2.67 53.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.588 α = 90 b = 76.755 β = 108.66 c = 107.083 γ = 90
Symmetry Space Group P 1 21 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 MARMOSAIC 225 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.979 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 46.01 98.8 0.063 25.7 3.6 130328 128719 2.5 19
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.86 90.3 0.38 2.5 2.6 11750
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT PDB ENTRY 3M8W 1.8 20 128653 6127 98.82 0.1697 0.1683 0.1715 0.1983 0.201 RANDOM 27.0423
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] 0.7 -0.98 -1.18 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.614 r_dihedral_angle_4_deg 13.433 r_dihedral_angle_3_deg 13.14 r_dihedral_angle_1_deg 5.398 r_scangle_it 2.283 r_scbond_it 1.319 r_angle_refined_deg 1.099 r_mcangle_it 0.707 r_mcbond_it 0.358 r_chiral_restr 0.074
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.614 r_dihedral_angle_4_deg 13.433 r_dihedral_angle_3_deg 13.14 r_dihedral_angle_1_deg 5.398 r_scangle_it 2.283 r_scbond_it 1.319 r_angle_refined_deg 1.099 r_mcangle_it 0.707 r_mcbond_it 0.358 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9195 Nucleic Acid Atoms Solvent Atoms 980 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement CNS refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing