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Crystal structure of a synthase 1 from Santalum album
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ONG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 Ammonium Sulfate, HEPES, MgCl2
Crystal Properties Matthews coefficient Solvent content 2.69 54.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.668 α = 90 b = 139.531 β = 90 c = 110.922 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2016-01-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13C1 1.0 NSRRC BL13C1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.6 25 99.9 0.037 0.04 0.017 18.3 5.8 87392
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 1.6 1.66 100 0.487 0.017 0.007 1 5.7
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2ONG 1.6 24.34 80141 4291 96.58 0.1597 0.1581 0.1711 0.1907 0.1999 RANDOM 26.348
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] 0.13 -0.22 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.873 r_dihedral_angle_4_deg 16.557 r_dihedral_angle_3_deg 14.848 r_dihedral_angle_1_deg 6.298 r_angle_other_deg 1.483 r_angle_refined_deg 1.44 r_chiral_restr 0.085 r_gen_planes_refined 0.012 r_bond_refined_d 0.01 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.873 r_dihedral_angle_4_deg 16.557 r_dihedral_angle_3_deg 14.848 r_dihedral_angle_1_deg 6.298 r_angle_other_deg 1.483 r_angle_refined_deg 1.44 r_chiral_restr 0.085 r_gen_planes_refined 0.012 r_bond_refined_d 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4271 Nucleic Acid Atoms Solvent Atoms 590 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing