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Prenyltransferase Ord1 D219A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9V4G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 0.1 M Bis-Tris, pH 5.5, 0.2 M Ammonium sulfate, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.2 44.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.879 α = 93.455 b = 72.425 β = 110.501 c = 83.774 γ = 90.085
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 EIGER X 16M 2023-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.980000 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.8 50 97.8 0.118 0.996 11.83 3.6 31241
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.97 97.2 0.712 0.771 3.09 3.7
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 9V4G 2.8 44.35 1.98 31239 1588 98 0.2307 0.224 0.2277 0.2539 0.2435 67.49
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 15.4778 f_angle_d 0.7244 f_chiral_restr 0.0449 f_plane_restr 0.006 f_bond_d 0.0039
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8567 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling MOLREP phasing