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rRNA methyltransferase aviRa from Streptomyces viridochromogenes at 2.4A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O9G PDB ENTRY 1O9G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.6 MES 6.6,PEG 20K 11%, pH 6.60
Crystal Properties Matthews coefficient Solvent content 2.14 39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.098 α = 90 b = 48.937 β = 99.05 c = 63.714 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 287 AREA DETECTOR BRUKER 2002-01-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200B
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 2.4 26.4 90 0.071 38.7 2.3 8039 2
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) 1 2.4 2.46 90 0.282 3.2 1.5
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 PDB ENTRY 1O9G 2.4 26.44 7709 382 90.1 0.211 0.209 0.2062 0.241 0.2385 RANDOM 49.48
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] -2.64 -0.55 2.77 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.981 r_scangle_it 3.112 r_mcangle_it 1.703 r_scbond_it 1.66 r_angle_refined_deg 1.188 r_mcbond_it 0.912 r_angle_other_deg 0.779 r_nbd_other 0.218 r_symmetry_vdw_other 0.214 r_nbd_refined 0.196
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.981 r_scangle_it 3.112 r_mcangle_it 1.703 r_scbond_it 1.66 r_angle_refined_deg 1.188 r_mcbond_it 0.912 r_angle_other_deg 0.779 r_nbd_other 0.218 r_symmetry_vdw_other 0.214 r_nbd_refined 0.196 r_xyhbond_nbd_refined 0.175 r_symmetry_vdw_refined 0.144 r_nbtor_other 0.083 r_symmetry_hbond_refined 0.065 r_chiral_restr 0.061 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1868 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing