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Crystal structure of VP5 from Haloarchaeal pleomorphic virus 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other HRPV6 VP5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 12% (w/v) PEG 4000, 0.1 M Na-HEPES pH 7.5 and 0.1 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.42 49.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.08 α = 90 b = 93.22 β = 90 c = 121.82 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 PIXEL DECTRIS PILATUS 6M 2010-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9778 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.46 46.6 81.4 0.126 0.069 10.2 4.6 16761 31.94
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 2.46 2.52 36.3 0.4 2.2 2.9
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 MOLECULAR REPLACEMENT THROUGHOUT HRPV6 VP5 2.46 46.6 16729 841 81.2 0.225 0.224 0.2326 0.241 0.2487 RANDOM 39.72
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] -2.3339 11.4216 -9.0877
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 2.57 t_omega_torsion 2.37 t_angle_deg 0.99 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 2.57 t_omega_torsion 2.37 t_angle_deg 0.99 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3740 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 18
Software Software Software Name Purpose BUSTER refinement xia2 data reduction xia2 data scaling PHASER phasing