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Inosine 5'-monophosphate dehydrogenase from Vibrio cholerae, deletion mutant, in complex with XMP and NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QNE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 1.03 M sodium/phosphate buffer, 0.15 M malate, 3% PEG-300
Crystal Properties Matthews coefficient Solvent content 2.33 47.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.262 α = 90 b = 91.262 β = 90 c = 171.214 γ = 90
Symmetry Space Group P 4 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 315r 2014-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9792 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.62 50 100 0.067 0.071 0.025 10.8 8.2 92477 92477 29.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.62 1.65 100 0.743 0.796 0.283 0.839 2.84 7.8 4551
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 MOLECULAR REPLACEMENT THROUGHOUT 4QNE 1.62 44.2 87862 4552 99.92 0.15345 0.152 0.166 0.18157 0.1934 RANDOM 23.896
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] 0.1 0.1 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.198 r_dihedral_angle_4_deg 18.088 r_dihedral_angle_3_deg 12.553 r_dihedral_angle_1_deg 6.062 r_long_range_B_refined 6.011 r_long_range_B_other 5.712 r_scangle_other 3.825 r_scbond_it 2.491 r_scbond_other 2.479 r_mcangle_it 2.369
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.198 r_dihedral_angle_4_deg 18.088 r_dihedral_angle_3_deg 12.553 r_dihedral_angle_1_deg 6.062 r_long_range_B_refined 6.011 r_long_range_B_other 5.712 r_scangle_other 3.825 r_scbond_it 2.491 r_scbond_other 2.479 r_mcangle_it 2.369 r_mcangle_other 2.369 r_angle_refined_deg 1.919 r_mcbond_it 1.604 r_mcbond_other 1.604 r_angle_other_deg 0.863 r_chiral_restr 0.1 r_bond_refined_d 0.015 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5029 Nucleic Acid Atoms Solvent Atoms 563 Heterogen Atoms 149
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection PDB_EXTRACT data extraction HKL-3000 data scaling HKL-3000 phasing MOLREP phasing