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Crystal Structure of Iridoid Synthase from Cantharanthus roseus in complex with NADPH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V6F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 298 Ammonium Acetate,Sodium Acetate trihydrate,Polyethylene Glycol 4000, Glycerol
Crystal Properties Matthews coefficient Solvent content 2.28 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.769 α = 90 b = 94.887 β = 90 c = 172.6 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 RAYONIX MX-300 2015-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1.0 NSRRC BL15A1
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 2 25 97.6 0.064 0.072 0.032 18.1 5 49651
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 2.07 91.1 0.396 0.441 0.191 0.947 5 4564
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 2V6F 2 25 47205 2403 97.1 0.1948 0.1921 0.2001 0.246 0.2481 RANDOM 45.914
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] -1.42 5.92 -4.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.299 r_dihedral_angle_4_deg 18.517 r_dihedral_angle_3_deg 16.767 r_dihedral_angle_1_deg 6.343 r_mcangle_it 4.668 r_mcbond_it 3.439 r_mcbond_other 3.435 r_angle_refined_deg 1.717 r_angle_other_deg 1.019 r_chiral_restr 0.108
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.299 r_dihedral_angle_4_deg 18.517 r_dihedral_angle_3_deg 16.767 r_dihedral_angle_1_deg 6.343 r_mcangle_it 4.668 r_mcbond_it 3.439 r_mcbond_other 3.435 r_angle_refined_deg 1.717 r_angle_other_deg 1.019 r_chiral_restr 0.108 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5707 Nucleic Acid Atoms Solvent Atoms 291 Heterogen Atoms 96
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing