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Inosine 5'-monophosphate dehydrogenase from Vibrio cholerae, deletion mutant, in complex with XMP
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 8 289 10% PEG 2000, 19.3% PEG 200, 0.05 M Tris-buffer, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.45 49.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.9 α = 90 b = 106.9 β = 90 c = 65.489 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 2014-05-23 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) 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 1.72 38.6 98.4 0.066 12.2 12.1 40250 40250 33.7
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 1.72 1.75 82.5 0.499 2.1 4.9 1623
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 4QNE 1.72 38.6 40207 40207 1992 98.43 0.168 0.168 0.1667 0.1782 0.1931 0.2015 RANDOM 35.722
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] -1.11 -1.11 2.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.039 r_dihedral_angle_4_deg 19.981 r_dihedral_angle_3_deg 14.969 r_dihedral_angle_1_deg 5.808 r_mcangle_it 2.866 r_mcbond_it 2.01 r_mcbond_other 2.008 r_angle_refined_deg 1.695 r_angle_other_deg 0.837 r_chiral_restr 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.039 r_dihedral_angle_4_deg 19.981 r_dihedral_angle_3_deg 14.969 r_dihedral_angle_1_deg 5.808 r_mcangle_it 2.866 r_mcbond_it 2.01 r_mcbond_other 2.008 r_angle_refined_deg 1.695 r_angle_other_deg 0.837 r_chiral_restr 0.1 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2187 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms 26
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing HKL-3000 phasing