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The 2.3 A resolution structure of the Sapporo virus RNA dependant RNA polymerase.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KHV PDB ENTRY 1KHV
Crystallization Crystal Properties Matthews coefficient Solvent content 2.29 45.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.434 α = 90 b = 93.881 β = 90 c = 94.771 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH 2005-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A EMBL/DESY, HAMBURG BW7A
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 2.3 30 99 0.11 5.2 3.9 27029 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 2.32 2.46 99 0.364 2.4 3.9
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 1KHV 2.3 66.67 22378 1209 99 0.174 0.171 0.1901 0.229 0.2378 RANDOM 19.78
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] -0.2 0.38 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.454 r_dihedral_angle_3_deg 20.304 r_dihedral_angle_4_deg 18.439 r_dihedral_angle_1_deg 7.279 r_scangle_it 5.987 r_scbond_it 3.939 r_angle_refined_deg 2.461 r_mcangle_it 2.455 r_mcbond_it 1.58 r_nbtor_refined 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.454 r_dihedral_angle_3_deg 20.304 r_dihedral_angle_4_deg 18.439 r_dihedral_angle_1_deg 7.279 r_scangle_it 5.987 r_scbond_it 3.939 r_angle_refined_deg 2.461 r_mcangle_it 2.455 r_mcbond_it 1.58 r_nbtor_refined 0.319 r_nbd_refined 0.284 r_symmetry_vdw_refined 0.242 r_chiral_restr 0.208 r_xyhbond_nbd_refined 0.193 r_symmetry_hbond_refined 0.164 r_bond_refined_d 0.031 r_gen_planes_refined 0.011 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_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 3766 Nucleic Acid Atoms Solvent Atoms 271 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOLREP phasing