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Crystal structure of benzophenone synthase from Garcinia mangostana L. pericarps reveals basis for substrate specificity and catalysis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CGK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 6.2 291 20% (w/v) PEG 3,350, 0.2 M ammonium iodide, pH 6.2
Crystal Properties Matthews coefficient Solvent content 2.28 46.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.81 α = 90 b = 98.33 β = 90 c = 112.024 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 315r 2015-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13C1 0.975 NSRRC BL13C1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.3 30 99.5 0.159 9.67 2.4 35272 17.52
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 99.7 0.49 3.14 2.4
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1CGK 2.301 24.347 35230 1763 99.452 0.172 0.1697 0.1762 0.2152 0.2181 16.241
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] -0.567 -0.124 0.691
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.244 r_dihedral_angle_4_deg 16.553 r_dihedral_angle_3_deg 14.829 r_dihedral_angle_1_deg 7.27 r_lrange_it 4.144 r_lrange_other 4.051 r_scangle_it 2.547 r_scangle_other 2.547 r_mcangle_other 1.91 r_mcangle_it 1.909
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.244 r_dihedral_angle_4_deg 16.553 r_dihedral_angle_3_deg 14.829 r_dihedral_angle_1_deg 7.27 r_lrange_it 4.144 r_lrange_other 4.051 r_scangle_it 2.547 r_scangle_other 2.547 r_mcangle_other 1.91 r_mcangle_it 1.909 r_scbond_it 1.526 r_scbond_other 1.525 r_angle_refined_deg 1.418 r_angle_other_deg 1.311 r_mcbond_it 1.122 r_mcbond_other 1.119 r_symmetry_xyhbond_nbd_refined 0.212 r_nbd_refined 0.206 r_symmetry_nbd_other 0.192 r_nbd_other 0.189 r_xyhbond_nbd_refined 0.183 r_symmetry_nbd_refined 0.182 r_nbtor_refined 0.155 r_symmetry_xyhbond_nbd_other 0.151 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5838 Nucleic Acid Atoms Solvent Atoms 317 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing