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Crystal structure of Grindelia robusta 7,13-copalyl diphosphate synthase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PYA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M sodium acetate
0.1 M Tris pH 8.5
30% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.29 46.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.07 α = 90 b = 79.11 β = 97.59 c = 88.44 γ = 90
Symmetry Space Group P 1 21 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 PILATUS3 2M 2017-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 0.99999 ALS 8.2.2
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 2.12 58.73 99.4 0.997 10.2 3.7 43361 32.05
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 2.12 2.16 0.566
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 2.12 58.73 1.35 43361 2178 99.44 0.1874 0.1852 0.1841 0.229 0.2268 47.51
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 16.2879 f_angle_d 0.5268 f_chiral_restr 0.0339 f_plane_restr 0.0154 f_bond_d 0.0034
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5790 Nucleic Acid Atoms Solvent Atoms 304 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement xia2 data reduction xia2 data scaling PHASER phasing