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Crystal structure of major capsid protein P 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 5.5 289 0.1 M sodium acetate, 1.1 M succinic acid, 1.0% PEG2000 MME, pH 5.5, VAPOR DIFFUSION, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.77 30.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.93 α = 90 b = 88.144 β = 90 c = 135.599 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 100 CCD RAYONIX MX-225 2010-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.99985 SSRF BL17U
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 99.1 0.089 29.8 3.7 36207 35882 -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 2.03 99.9 0.231 8.3 3.9 1727
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 (All) 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 36.95 36207 33925 1789 98.75 0.20073 0.20073 0.19916 0.2005 0.23154 0.2321 RANDOM 22.745
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] 0.19 -0.22 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.447 r_dihedral_angle_4_deg 15.477 r_dihedral_angle_3_deg 12.307 r_scangle_it 5.338 r_dihedral_angle_1_deg 3.964 r_scbond_it 3.441 r_mcangle_it 2.327 r_mcbond_it 1.362 r_angle_refined_deg 1.245 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.447 r_dihedral_angle_4_deg 15.477 r_dihedral_angle_3_deg 12.307 r_scangle_it 5.338 r_dihedral_angle_1_deg 3.964 r_scbond_it 3.441 r_mcangle_it 2.327 r_mcbond_it 1.362 r_angle_refined_deg 1.245 r_chiral_restr 0.089 r_gen_planes_refined 0.011 r_bond_refined_d 0.008 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 4870 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling