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Crystal structure of the Arg101Ala mutant protein of Rhesus rotavirus VP8*
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KQR RRV VP8* PDB code 1KQR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 303 1.7M (NH4)2SO4, 2.4% v/v PEG 400, 0.1M PIPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal Properties Matthews coefficient Solvent content 2.14 42.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.531 α = 90 b = 48.531 β = 90 c = 131.403 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 295 CCD BRUKER SMART 6000 mirrors 2004-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE MACSCIENCE 1.5418
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 1.9 65 91.7 0.048 11.8 12.7 12064
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) 1.9 2.04 63 0.107 4.7 1521
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 FOURIER SYNTHESIS THROUGHOUT RRV VP8* PDB code 1KQR 1.9 45.64 11421 587 91.67 0.1629 0.16075 0.1595 0.20586 0.2044 RANDOM 18.025
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] -0.03 -0.03 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.627 r_dihedral_angle_3_deg 12.073 r_dihedral_angle_1_deg 6.142 r_dihedral_angle_4_deg 2.857 r_scangle_it 2.648 r_scbond_it 1.786 r_angle_refined_deg 1.217 r_mcangle_it 1.115 r_mcbond_it 0.693 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.627 r_dihedral_angle_3_deg 12.073 r_dihedral_angle_1_deg 6.142 r_dihedral_angle_4_deg 2.857 r_scangle_it 2.648 r_scbond_it 1.786 r_angle_refined_deg 1.217 r_mcangle_it 1.115 r_mcbond_it 0.693 r_nbtor_refined 0.308 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.146 r_xyhbond_nbd_refined 0.133 r_symmetry_hbond_refined 0.121 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1274 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data collection SAINT data reduction LSCALE data scaling AMoRE phasing