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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 2.34 47.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.868 α = 90 b = 76.617 β = 101.55 c = 77.158 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 PILATUS 6M-F 2015-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
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 1.2 76.62 97.3 0.069 0.046 0.995 7.2 3.1 237667
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 1.2 1.22 88.7 0.694 0.58 0.532 1.2 2
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 1.2 75.71 225776 11862 97.14 0.11737 0.11671 0.1163 0.13021 0.1299 RANDOM 15.394
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] 0.33 -0.04 -0.18 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.339 r_dihedral_angle_4_deg 14.994 r_dihedral_angle_3_deg 12.526 r_dihedral_angle_1_deg 6.108 r_rigid_bond_restr 3.965 r_long_range_B_refined 3.89 r_long_range_B_other 3.89 r_scangle_other 3.281 r_scbond_it 2.768 r_scbond_other 2.767
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.339 r_dihedral_angle_4_deg 14.994 r_dihedral_angle_3_deg 12.526 r_dihedral_angle_1_deg 6.108 r_rigid_bond_restr 3.965 r_long_range_B_refined 3.89 r_long_range_B_other 3.89 r_scangle_other 3.281 r_scbond_it 2.768 r_scbond_other 2.767 r_mcangle_it 2.14 r_mcangle_other 2.14 r_angle_refined_deg 1.942 r_mcbond_it 1.633 r_mcbond_other 1.633 r_angle_other_deg 1.609 r_chiral_restr 0.112 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.005 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5363 Nucleic Acid Atoms Solvent Atoms 892 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing