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Crystal Structure of Iridoid Synthase from Cantharanthus roseus in complex with NAD+ and 10-oxogeranial
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, HANGING DROP 4.6 298 Ammonium Acetate, Sodium Acetate trihydrate, Polyethylene Glycol 4000, Glycerol
Crystal Properties Matthews coefficient Solvent content 2.29 46.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.056 α = 90 b = 94.629 β = 90 c = 172.818 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 2015-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0 NSRRC BL13B1
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 2.2 25 99.7 0.048 0.055 0.026 10.4 4.2 41981
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 2.28 98.3 0.329 0.375 0.179 0.929 4.1 3727
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 2.2 25 36479 1945 99.58 0.1658 0.16348 0.1699 0.20989 0.2102 RANDOM 50.254
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] -0.17 2.98 -2.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.412 r_dihedral_angle_4_deg 20.704 r_dihedral_angle_3_deg 17.063 r_long_range_B_other 9.016 r_long_range_B_refined 9.015 r_scangle_other 7.242 r_dihedral_angle_1_deg 6.585 r_mcangle_it 5.704 r_mcangle_other 5.704 r_scbond_it 4.931
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.412 r_dihedral_angle_4_deg 20.704 r_dihedral_angle_3_deg 17.063 r_long_range_B_other 9.016 r_long_range_B_refined 9.015 r_scangle_other 7.242 r_dihedral_angle_1_deg 6.585 r_mcangle_it 5.704 r_mcangle_other 5.704 r_scbond_it 4.931 r_scbond_other 4.93 r_mcbond_other 4.058 r_mcbond_it 4.057 r_angle_refined_deg 1.763 r_angle_other_deg 1.044 r_chiral_restr 0.115 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.004 r_gen_planes_other 0.004 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5741 Nucleic Acid Atoms Solvent Atoms 219 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing