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geranyl pyrophosphate C6-methyltransferase BezA binding with S-adenosylhomocysteine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7FBH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M HEPES (pH 7.5), 25% PEG3350, 0.2 M CH3COONH4. 0.01 M spermine tetrahydrochloride
Soaking using 0.1 M HEPES (pH7.5), 35% PEG3350, 1.0 mM SAH.
Crystal Properties Matthews coefficient Solvent content 2.34 47.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.309 α = 90 b = 117.426 β = 90 c = 195.557 γ = 90
Symmetry Space Group I 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 95 PIXEL DECTRIS EIGER X 4M 2019-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.0 Photon Factory BL-1A
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 2.56 50.34 100 0.15 0.15 0.055 0.996 11.2 7.5 30941 40.1
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 2.56 2.67 100 0.864 0.926 0.33 0.835 2.5 7.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 7FBH 2.56 50.34 30941 1952 97.59 0.1828 0.1782 0.1755 0.2537 0.2483 44.08
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 13.2823 f_angle_d 1.0872 f_chiral_restr 0.0566 f_plane_restr 0.0094 f_bond_d 0.0076
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6615 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 123
Software Software Software Name Purpose PHENIX refinement PHENIX model building XDS data reduction Aimless data scaling PHASER phasing