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PmHMGR bound to mevalonate, CoA, and NAD, buffer-exchanged to ammonium acetate environment at pH 6.7
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 6.7 293.15 1.2 M ammonium sulfate, 100 mM N-(2-Acetamido)iminodiacetic acid and 10 % glycerol
Crystal Properties Matthews coefficient Solvent content 2.66 53.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 225.674 α = 90 b = 225.674 β = 90 c = 225.674 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 2020-10-15 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) Rrim I (All) 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 1.93 50 100 0.111 0.114 0.025 0.995 6.9 19.9 73036
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 1.93 2 100 3.56 3.656 0.831 0.309 19.1
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 FREE R-VALUE 1.93 48.11 1.35 62447 3077 85.82 0.1801 0.1781 0.1785 0.2173 0.217
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 20.412 f_angle_d 0.883 f_chiral_restr 0.051 f_plane_restr 0.008 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5875 Nucleic Acid Atoms Solvent Atoms 448 Heterogen Atoms 117
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing