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Crystal structure of major capsid protein S domain from rabbit hemorrhagic disease virus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GH8 PDB ENTRY 2GH8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 289 0.2 M magnesium chloride, 0.1 M HEPES sodium, 30% PEG400, pH 7.0, VAPOR DIFFUSION, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.79 31.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.734 α = 90 b = 48.362 β = 100.95 c = 65.163 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2010-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
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 50 99.77 0.086 25.7 7.4 24872 24815 -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 2.07 99.8 0.404 3.97 6.8
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 2GH8 2 49.35 24872 24813 1330 99.79 0.20257 0.2005 0.201 0.24064 0.2385 RANDOM 23.968
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] 0.01 0.03 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.424 r_dihedral_angle_3_deg 15.48 r_dihedral_angle_4_deg 14.489 r_dihedral_angle_1_deg 6.654 r_scangle_it 5.925 r_scbond_it 3.82 r_mcangle_it 2.631 r_angle_refined_deg 2.109 r_mcbond_it 1.559 r_chiral_restr 0.172
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.424 r_dihedral_angle_3_deg 15.48 r_dihedral_angle_4_deg 14.489 r_dihedral_angle_1_deg 6.654 r_scangle_it 5.925 r_scbond_it 3.82 r_mcangle_it 2.631 r_angle_refined_deg 2.109 r_mcbond_it 1.559 r_chiral_restr 0.172 r_bond_refined_d 0.027 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2520 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms
Software Software Software Name Purpose SERGUI data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling