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Structure of catharanthine synthase - an alpha-beta hydrolase from Catharanthus roseus with a cleaviminium intermediate bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6RS4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 NULL
Crystal Properties Matthews coefficient Solvent content 2.6 52.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.54 α = 90 b = 121.03 β = 99.02 c = 157.98 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 6M 2016-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.19 52.01 98.3 0.093 0.1 0.038 0.999 14.1 7 152727 41.2
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 2.19 2.23 97.7 1.129 1.219 0.457 0.559 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 6RS4 2.19 52.01 145106 7594 98.1 0.1959 0.1939 0.2022 0.2342 0.238 RANDOM 62.531
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] -0.78 2.8 0.88 -0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.655 r_dihedral_angle_4_deg 20.943 r_dihedral_angle_3_deg 14.221 r_dihedral_angle_1_deg 7.215 r_angle_refined_deg 1.522 r_angle_other_deg 1.269 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.655 r_dihedral_angle_4_deg 20.943 r_dihedral_angle_3_deg 14.221 r_dihedral_angle_1_deg 7.215 r_angle_refined_deg 1.522 r_angle_other_deg 1.269 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19468 Nucleic Acid Atoms Solvent Atoms 388 Heterogen Atoms 276
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing