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Crystal Structure of Norwalk Virus Polymerase (MgSO4 crystal form)
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, magnesium sulfate, Tris-Cl, glycerol, CHAPS, 2-mercaptoethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.83 56.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.05 α = 90 b = 109.14 β = 90 c = 112.044 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 110 IMAGE PLATE MARRESEARCH mirrors 2003-12-01 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 2.95 20 100 0.115 0.115 16.7 6.7 27684 27684 -3 76.6
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 2.95 3.06 100 0.618 0.618 3.2 6.7 2688
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 2.95 20 27637 26218 1419 100 0.21857 0.21522 0.2092 0.2799 0.2692 RANDOM 17.668
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] -1.22 1.85 -0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.774 r_scangle_it 3.396 r_scbond_it 2.162 r_mcangle_it 1.633 r_angle_refined_deg 1.146 r_mcbond_it 0.891 r_symmetry_vdw_refined 0.256 r_nbd_refined 0.217 r_xyhbond_nbd_refined 0.153 r_symmetry_hbond_refined 0.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.774 r_scangle_it 3.396 r_scbond_it 2.162 r_mcangle_it 1.633 r_angle_refined_deg 1.146 r_mcbond_it 0.891 r_symmetry_vdw_refined 0.256 r_nbd_refined 0.217 r_xyhbond_nbd_refined 0.153 r_symmetry_hbond_refined 0.091 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7887 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling BEAST phasing