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X-ray crystal structure of the Mg-bound 3-keto-L-gulonate-6-phosphate decarboxylase from Vibrio cholerae O1 biovar El Tor str. N16961
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IEB PDB entry 3IEB
Crystallization Crystal Properties Matthews coefficient Solvent content 2.6 52.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.305 α = 90 b = 95.711 β = 90 c = 125.577 γ = 90
Symmetry Space Group P 21 21 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 ADSC QUANTUM 315r mirrors 2009-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9794 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 1.8 40 99.9 0.113 16.4 4.7 92645 92551 2 2 29
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 1.8 1.83 99.8 0.72 2.1 4.7 4577
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3IEB 1.8 40 2 2 87622 4619 99.82 0.17 0.16517 0.16318 0.1733 0.20233 0.2117 RANDOM 14.291
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] -1.23 0.45 0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.211 r_dihedral_angle_4_deg 17.664 r_dihedral_angle_3_deg 13.298 r_dihedral_angle_1_deg 5.651 r_scangle_it 4.794 r_scbond_it 3.089 r_mcangle_it 1.745 r_angle_refined_deg 1.642 r_mcbond_it 0.984 r_angle_other_deg 0.959
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.211 r_dihedral_angle_4_deg 17.664 r_dihedral_angle_3_deg 13.298 r_dihedral_angle_1_deg 5.651 r_scangle_it 4.794 r_scbond_it 3.089 r_mcangle_it 1.745 r_angle_refined_deg 1.642 r_mcbond_it 0.984 r_angle_other_deg 0.959 r_mcbond_other 0.322 r_chiral_restr 0.101 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6450 Nucleic Acid Atoms Solvent Atoms 766 Heterogen Atoms 97
Software Software Software Name Purpose SBC-Collect data collection MOLREP phasing ARP/wARP model building Coot model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling