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Crystal structure of 10-Hydroxygeraniol Dehydrogenase from Cantharanthus roseus in complex with NADP+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YQD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 294 MES, PEG 6000, 2-Methyl-2,4-pentanediol, Sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.68 54.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.18 α = 90 b = 53.18 β = 90 c = 252.773 γ = 120
Symmetry Space Group P 32 1 2
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 2M 2018-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.0393 ELETTRA 5.2R
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 2.41 46.06 99.9 0.124 0.146 0.075 0.996 10.9 6.8 16295 39.965
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 2.41 2.5 99.4 0.849 0.99 0.5 0.919 2.7 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 1YQD 2.41 42.16 15375 849 99.49 0.21017 0.20713 0.2167 0.26611 0.268 RANDOM 55.796
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] 0.23 0.12 0.23 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.879 r_dihedral_angle_3_deg 19.247 r_dihedral_angle_4_deg 11.332 r_dihedral_angle_1_deg 8.282 r_long_range_B_refined 5.758 r_long_range_B_other 5.756 r_mcangle_it 2.569 r_mcangle_other 2.569 r_scangle_other 2.247 r_angle_refined_deg 2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.879 r_dihedral_angle_3_deg 19.247 r_dihedral_angle_4_deg 11.332 r_dihedral_angle_1_deg 8.282 r_long_range_B_refined 5.758 r_long_range_B_other 5.756 r_mcangle_it 2.569 r_mcangle_other 2.569 r_scangle_other 2.247 r_angle_refined_deg 2 r_mcbond_it 1.491 r_mcbond_other 1.489 r_angle_other_deg 1.348 r_scbond_it 1.321 r_scbond_other 1.321 r_chiral_restr 0.088 r_bond_refined_d 0.014 r_bond_other_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 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 2689 Nucleic Acid Atoms Solvent Atoms 28 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing