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geniposidic acid O-methyltransferase complexed with SAH and geniposidic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6C8R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 281 0.1M BIS-TRIS pH6.0, 36% v/v Polypropylene glycol PEG 400
Crystal Properties Matthews coefficient Solvent content 2.38 48.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.825 α = 90 b = 103.086 β = 103.283 c = 84.203 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 EIGER X 16M 2022-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.97903 SSRF BL10U2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.958 64.3 89.8 0.071 0.997 7 2.8 50211
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.958 2.06 0.58 0.637 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.958 64.232 48027 2385 85.825 0.202 0.1999 0.2037 0.2336 0.2403 29.544
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] 2.246 0.588 -2.548 0.022
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.474 r_dihedral_angle_3_deg 14.708 r_dihedral_angle_1_deg 6.05 r_dihedral_angle_2_deg 6.035 r_lrange_it 4.169 r_lrange_other 4.168 r_scangle_it 1.266 r_scangle_other 1.265 r_mcangle_it 1.093 r_mcangle_other 1.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.474 r_dihedral_angle_3_deg 14.708 r_dihedral_angle_1_deg 6.05 r_dihedral_angle_2_deg 6.035 r_lrange_it 4.169 r_lrange_other 4.168 r_scangle_it 1.266 r_scangle_other 1.265 r_mcangle_it 1.093 r_mcangle_other 1.093 r_angle_refined_deg 1.077 r_scbond_it 0.752 r_scbond_other 0.752 r_mcbond_it 0.631 r_mcbond_other 0.631 r_angle_other_deg 0.395 r_nbd_other 0.251 r_nbd_refined 0.204 r_symmetry_nbd_refined 0.198 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.185 r_symmetry_xyhbond_nbd_refined 0.131 r_xyhbond_nbd_refined 0.13 r_symmetry_nbtor_other 0.076 r_chiral_restr_other 0.055 r_chiral_restr 0.054 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5137 Nucleic Acid Atoms Solvent Atoms 254 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling MOLREP phasing