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The crystal structure of oxidoreductase (Gfo/Idh/MocA family) from Streptococcus pneumoniae TIGR4 in complex with NADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IQ0 PDB ENTRY:4IQ0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 289 0.1M Sodium Acetate:HCl, 3.5M sodium format, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.8 67.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.768 α = 90 b = 195.905 β = 90 c = 349.301 γ = 90
Symmetry Space Group F 2 2 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 210r mirror 2012-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97910 APS 19-BM
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 1.95 36.5 97.2 0.081 28 4.7 117182 117182 -5
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 1.95 1.98 98.4 0.731 1.52 3.4 5848
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 MOLECULAR REPLACEMENT PDB ENTRY:4IQ0 1.95 36.174 1.33 116005 116005 5837 95.62 0.1774 0.1759 0.177 0.2067 0.2068 random
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.423 f_angle_d 1.05 f_chiral_restr 0.073 f_bond_d 0.007 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7650 Nucleic Acid Atoms Solvent Atoms 624 Heterogen Atoms 205
Software Software Software Name Purpose SBC-Collect data collection MOLREP phasing PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling