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Crystal Structure of Norwalk Virus Polymerase (Triclinic)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KHV PDB ENTRY 1KHV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 PEG 8000, ammonium sulfate, Tris-Cl, glycerol, 2-mercaptoethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.59 52.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.144 α = 104.36 b = 59.914 β = 92.49 c = 100.095 γ = 111.91
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 IMAGE PLATE MARRESEARCH mirrors 2003-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.17 40 95.1 0.042 0.042 24.4 4.1 57284 57284 -3 25.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.17 2.25 86.9 0.147 0.147 3.5 1.4 5246
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 1KHV 2.17 35.58 54384 54384 2892 95.1 0.19716 0.19412 0.1981 0.25552 0.2593 RANDOM 21.047
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] 0.02 0.71 -0.94 -0.08 -1.65 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.262 r_scangle_it 4.182 r_scbond_it 2.998 r_mcangle_it 1.925 r_mcbond_it 1.179 r_angle_refined_deg 1.022 r_nbd_refined 0.192 r_symmetry_vdw_refined 0.129 r_symmetry_hbond_refined 0.125 r_xyhbond_nbd_refined 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.262 r_scangle_it 4.182 r_scbond_it 2.998 r_mcangle_it 1.925 r_mcbond_it 1.179 r_angle_refined_deg 1.022 r_nbd_refined 0.192 r_symmetry_vdw_refined 0.129 r_symmetry_hbond_refined 0.125 r_xyhbond_nbd_refined 0.12 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7887 Nucleic Acid Atoms Solvent Atoms 434 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling BEAST phasing