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Yokose virus Methyltransferase in complex with AdoMet
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R6A PDB ENTRY 1R6A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 2% PEG 400, 1.5M ammonium sulphate, 100mM HEPES-Na pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.2 44.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.912 α = 90 b = 68.912 β = 90 c = 50.806 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 neutron 100 CCD ADSC QUANTUM 210 2007-04-26 M LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.7 51 98.7 24.6 10.9 30809 29342 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.79 91.1 3.1 8.6 3984
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 1R6A 1.7 20 29211 27820 1477 98.67 0.16863 0.16705 0.1716 0.1981 0.1928 RANDOM 19.949
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] -0.12 -0.06 -0.12 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.992 r_dihedral_angle_4_deg 18.143 r_dihedral_angle_3_deg 13.056 r_dihedral_angle_1_deg 5.203 r_scangle_it 3.188 r_scbond_it 1.986 r_angle_other_deg 1.433 r_angle_refined_deg 1.367 r_mcangle_it 1.31 r_mcbond_it 0.711
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.992 r_dihedral_angle_4_deg 18.143 r_dihedral_angle_3_deg 13.056 r_dihedral_angle_1_deg 5.203 r_scangle_it 3.188 r_scbond_it 1.986 r_angle_other_deg 1.433 r_angle_refined_deg 1.367 r_mcangle_it 1.31 r_mcbond_it 0.711 r_mcbond_other 0.197 r_chiral_restr 0.073 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_gen_planes_other 0.001 r_bond_other_d 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2049 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 60
Software Software Software Name Purpose MOSFLM data reduction MOLREP phasing REFMAC refinement SCALA data scaling