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Structure of the class II 3-hydroxy-3-methylglutaryl-CoA reductase from Streptococcus pneumoniae bound to NADPH in open conformations
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QAE PDB ENTRY 3QAE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295 100 mM Tris, pH 8.5, 100-250 mM lithium sulfate, 30-40% PEG4000
Crystal Properties Matthews coefficient Solvent content 2.1 41.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.99 α = 108.16 b = 84 β = 100.6 c = 94.21 γ = 109.12
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 PIXEL DECTRIS EIGER X 16M 2017-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9792 APS 24-ID-E
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 72.72 93.2 0.1159 5.02 2.1 95302 20.86
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 2.07 92.4 0.4474 1.88 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB ENTRY 3QAE 2 72.72 1.98 95287 4683 93.2 0.167 0.164 0.1655 0.224 0.2243
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 13.755 f_angle_d 1.243 f_chiral_restr 0.047 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11861 Nucleic Acid Atoms Solvent Atoms 1653 Heterogen Atoms 72
Software Software Software Name Purpose PHENIX refinement iMOSFLM data reduction Aimless data scaling PHENIX phasing