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Iridoid synthase from Catharanthus roseus - ligand free structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DCU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 NULL
Crystal Properties Matthews coefficient Solvent content 2.44 49.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.2 α = 90 b = 141.2 β = 90 c = 106.05 γ = 120
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 PILATUS 6M 2014-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9000 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 70.6 100 0.124 0.041 0.999 16.2 10.2 32009 17.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.95 99.7 0.986 0.324 0.799 2.4 10.2 2330
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 5DCU 1.9 70.6 30404 1605 99.95 0.1777 0.1761 0.1857 0.2088 0.2151 RANDOM 30
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] 0.11 0.06 0.11 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.036 r_dihedral_angle_4_deg 21.346 r_dihedral_angle_3_deg 12.074 r_dihedral_angle_1_deg 6.195 r_angle_refined_deg 1.533 r_mcangle_it 1.025 r_angle_other_deg 0.969 r_mcbond_it 0.587 r_mcbond_other 0.587 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.036 r_dihedral_angle_4_deg 21.346 r_dihedral_angle_3_deg 12.074 r_dihedral_angle_1_deg 6.195 r_angle_refined_deg 1.533 r_mcangle_it 1.025 r_angle_other_deg 0.969 r_mcbond_it 0.587 r_mcbond_other 0.587 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2796 Nucleic Acid Atoms Solvent Atoms 322 Heterogen Atoms 16
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing XDS data reduction