☰ Navigation Tabs
Crystal Structure of Norwalk Virus Polymerase (Metal-free, Centered Orthorhombic)
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, CHAPS, 2-mercaptoethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.66 53.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.27 α = 90 b = 115.24 β = 90 c = 91.9 γ = 90
Symmetry Space Group C 2 2 21
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 2003-10-01 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 2.3 40 98.8 0.075 0.075 19.8 8 27003 27003 -3 40
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 2.3 2.37 91.3 0.402 0.402 2.3 3.5 2054
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1KHV 2.3 36.04 25374 25374 1596 100 0.23054 0.22672 0.29087 0.2683 RANDOM 23.817
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] -0.15 -5.55 5.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.509 r_scangle_it 3.238 r_scbond_it 2.39 r_mcangle_it 1.844 r_angle_refined_deg 1.07 r_mcbond_it 0.991 r_nbd_refined 0.194 r_symmetry_hbond_refined 0.192 r_symmetry_vdw_refined 0.138 r_xyhbond_nbd_refined 0.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.509 r_scangle_it 3.238 r_scbond_it 2.39 r_mcangle_it 1.844 r_angle_refined_deg 1.07 r_mcbond_it 0.991 r_nbd_refined 0.194 r_symmetry_hbond_refined 0.192 r_symmetry_vdw_refined 0.138 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3939 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling BEAST phasing