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Crystal structure of Penicillium verruculosum copalyl diphosphate synthase (PvCPS) alpha prenyltransferase domain variant, S723T, bound with non-productive isopentenyl diphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6V0K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 0.1 M sodium citrate pH 5.6
0.015 M sodium citrate tribasic dihydrate
2.5% tacsimate pH 5.0
20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 4.21 70.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 189.801 α = 90 b = 189.801 β = 90 c = 56.483 γ = 120
Symmetry Space Group P 3 2 1
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 PILATUS 6M-F 2021-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.98 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 62.13 100 0.999 10.96 9.7 762371 26.55
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.071 0.505 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 6V0K 2 62.13 1.34 153774 3923 99.96 0.176 0.1755 0.1758 0.1949 0.1945 32.75
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 10.6211 f_angle_d 0.8098 f_chiral_restr 0.0452 f_bond_d 0.0071 f_plane_restr 0.0068
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4837 Nucleic Acid Atoms Solvent Atoms 533 Heterogen Atoms 28
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction Aimless data scaling PHASER phasing