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Papaver somniferum O-methyltransferase 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6I5Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 PEG 3350, diammonium citrate
Crystal Properties Matthews coefficient Solvent content 2.28 46.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.221 α = 90 b = 75.942 β = 101.62 c = 76.571 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 PILATUS3 6M 2015-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 1.29 75.94 95.5 0.052 0.037 0.997 9.5 3.6 184110
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 1.29 1.31 92.3 0.813 0.604 0.511 1.7 3.6
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 6I5Q 1.29 75.11 173869 9211 95.34 0.12596 0.12431 0.1246 0.15775 0.1586 RANDOM 17.311
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] -0.43 0.16 -0.03 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.174 r_dihedral_angle_4_deg 17.777 r_dihedral_angle_3_deg 12.799 r_dihedral_angle_1_deg 6.166 r_scangle_other 4.694 r_rigid_bond_restr 4.626 r_long_range_B_refined 4.262 r_long_range_B_other 4.262 r_scbond_it 3.958 r_scbond_other 3.958
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.174 r_dihedral_angle_4_deg 17.777 r_dihedral_angle_3_deg 12.799 r_dihedral_angle_1_deg 6.166 r_scangle_other 4.694 r_rigid_bond_restr 4.626 r_long_range_B_refined 4.262 r_long_range_B_other 4.262 r_scbond_it 3.958 r_scbond_other 3.958 r_mcangle_it 2.847 r_mcangle_other 2.846 r_mcbond_it 2.468 r_mcbond_other 2.467 r_angle_refined_deg 1.962 r_angle_other_deg 1.631 r_chiral_restr 0.13 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5342 Nucleic Acid Atoms Solvent Atoms 596 Heterogen Atoms 102
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing