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Catechol O-methyltransferase from Streptomyces avermitilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DUW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.1M MIB(Malonic acid,Imidazole,Boric acid) pH6.0; 25% PEG1500
Crystal Properties Matthews coefficient Solvent content 2.25 45.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.457 α = 90 b = 168.744 β = 101.487 c = 57.242 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 2022-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
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 1.5 46.71 96.2 0.051 0.999 22.6 7.1 131969
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 1.5 1.53 0.278 0.967
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.5 46.71 131918 6583 96.071 0.168 0.1669 0.1936 0.201 14.486
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] -0.356 -0.445 -0.57 1.023
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.893 r_dihedral_angle_4_deg 15.67 r_dihedral_angle_3_deg 12.487 r_dihedral_angle_1_deg 5.512 r_lrange_it 4.655 r_lrange_other 4.654 r_scangle_it 3.684 r_scangle_other 3.683 r_scbond_it 2.435 r_scbond_other 2.435
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.893 r_dihedral_angle_4_deg 15.67 r_dihedral_angle_3_deg 12.487 r_dihedral_angle_1_deg 5.512 r_lrange_it 4.655 r_lrange_other 4.654 r_scangle_it 3.684 r_scangle_other 3.683 r_scbond_it 2.435 r_scbond_other 2.435 r_mcangle_other 2.055 r_mcangle_it 2.053 r_angle_refined_deg 1.825 r_angle_other_deg 1.563 r_mcbond_it 1.42 r_mcbond_other 1.411 r_symmetry_nbd_refined 0.269 r_nbd_refined 0.225 r_nbd_other 0.215 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.154 r_symmetry_xyhbond_nbd_refined 0.148 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6759 Nucleic Acid Atoms Solvent Atoms 712 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing