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Structure of PmHMGR bound to mevalonate, CoA and NAD 5 minutes after reaction initiation at pH 9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4I64
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 293.15 1.2 M ammonium sulfate, 100 mM N-(2-Acetamido)iminodiacetic acid and 10 % glycerol
Crystal Properties Matthews coefficient Solvent content 2.63 53.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 225.988 α = 90 b = 225.988 β = 90 c = 225.988 γ = 90
Symmetry Space Group I 41 3 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 PIXEL DECTRIS PILATUS3 6M 2018-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rpim I (All) CC (Half) 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 2.06 50 99.1 0.1054 0.1114 0.03596 0.998 10.6 9.5 60173 23.45
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 2.06 2.13 91.3 0.759 0.813 0.285 0.607 8.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.07 48.18 1.35 59238 2994 98.69 0.2167 0.2151 0.2197 0.2484 0.2515
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 9.009 f_angle_d 0.595 f_chiral_restr 0.04 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5910 Nucleic Acid Atoms Solvent Atoms 429 Heterogen Atoms 219
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling HKL-2000 data reduction PDB_EXTRACT data extraction PHASER phasing