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The crystal structure of uncharacterized Ribose 5-phosphate isomerase RpiB from Streptococcus pneumoniae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 298 0.1M Na acetate pH 4.6, 0.4M Mg formate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.13 42.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.915 α = 90 b = 52.416 β = 90 c = 85.018 γ = 90
Symmetry Space Group P 21 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 ADSC QUANTUM 315 mirrors 2007-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9798 APS 19-ID
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 2.01 85.13 99.5 0.124 21.86 9.3 27060 26774 24
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 2.01 2.07 91.46 0.375 4.1 8.1 1873
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 2.01 85.13 26774 26774 1421 98.94 0.17902 0.17691 0.1786 0.21807 0.2189 RANDOM 23.135
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] -0.25 -0.21 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.877 r_dihedral_angle_4_deg 25.683 r_dihedral_angle_3_deg 13.592 r_dihedral_angle_1_deg 4.949 r_scangle_it 3.022 r_scbond_it 1.973 r_angle_refined_deg 1.204 r_mcangle_it 1.103 r_mcbond_it 0.77 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.877 r_dihedral_angle_4_deg 25.683 r_dihedral_angle_3_deg 13.592 r_dihedral_angle_1_deg 4.949 r_scangle_it 3.022 r_scbond_it 1.973 r_angle_refined_deg 1.204 r_mcangle_it 1.103 r_mcbond_it 0.77 r_nbtor_refined 0.304 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.19 r_xyhbond_nbd_refined 0.146 r_symmetry_hbond_refined 0.14 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3269 Nucleic Acid Atoms Solvent Atoms 271 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling MLPHARE phasing