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Crystal structure of a synthase 1 from Santalum album in complex with ligand
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 2.53 51.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.437 α = 90 b = 139.487 β = 90 c = 110.93 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 1.78 25 99.1 0.05 0.059 0.031 12 3.6 62747
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 1.78 1.84 99.8 0.481 0.561 0.286 0.786 3.7
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 1.78 24.94 59554 3148 98.87 0.169 0.167 0.1729 0.2057 0.209 RANDOM 30.895
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] 0.26 -0.37 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.172 r_dihedral_angle_4_deg 15.963 r_dihedral_angle_3_deg 14.493 r_dihedral_angle_1_deg 6.327 r_angle_refined_deg 1.469 r_angle_other_deg 0.521 r_chiral_restr 0.283 r_gen_planes_refined 0.013 r_bond_refined_d 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.172 r_dihedral_angle_4_deg 15.963 r_dihedral_angle_3_deg 14.493 r_dihedral_angle_1_deg 6.327 r_angle_refined_deg 1.469 r_angle_other_deg 0.521 r_chiral_restr 0.283 r_gen_planes_refined 0.013 r_bond_refined_d 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4227 Nucleic Acid Atoms Solvent Atoms 434 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing