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Crystal structure of Meaban virus nucleoside-2'-O-methyltransferase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R6A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 20% PEGMME 2000, nickel chloride 0.01M, Tris 0.1 M , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.47 50.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.977 α = 90 b = 82.977 β = 90 c = 170.202 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 Liquid nitrogen cooled channel-cut silicon monochromator and a cylindrical grazing incidence mirror 2006-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.954 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.9 40 95.4 0.095 12.4 3.2 24302 24302
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.9 3.06 96.8 0.526 3.1 3.2 3582
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 (All) 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 1R6A 2.9 37.85 24302 23074 1213 95.4 0.23444 0.23444 0.23071 0.2239 0.30597 0.3024 RANDOM 58.639
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] -3.66 -3.66 7.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.291 r_dihedral_angle_3_deg 19.5 r_dihedral_angle_4_deg 17.942 r_dihedral_angle_1_deg 5.253 r_scangle_it 1.968 r_angle_refined_deg 1.106 r_scbond_it 1.096 r_mcangle_it 0.848 r_mcbond_it 0.459 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.291 r_dihedral_angle_3_deg 19.5 r_dihedral_angle_4_deg 17.942 r_dihedral_angle_1_deg 5.253 r_scangle_it 1.968 r_angle_refined_deg 1.106 r_scbond_it 1.096 r_mcangle_it 0.848 r_mcbond_it 0.459 r_nbtor_refined 0.303 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.182 r_xyhbond_nbd_refined 0.156 r_symmetry_hbond_refined 0.102 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8296 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 108
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction CCP4 data scaling