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Crystal structure of Pseudorabies virus glycoprotein B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GUM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 0.1M Tris pH 8.5, 7% PEG 4,000, 0.6M LiCl
Crystal Properties Matthews coefficient Solvent content 3.19 62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.89 α = 90 b = 99.89 β = 90 c = 272.8 γ = 120
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 PILATUS3 6M Toroidal mirror 2015-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97625 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 2.69 46.15 99.6 0.074 0.055 0.98 14.99 5.3 28086 86.38
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.69 2.85 98.3 0.523 0.386 0.82 2.33
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 2GUM 2.7 46.15 27695 1385 99.4 0.195 0.193 0.1911 0.236 0.2352 RANDOM 73.49
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] -10.04 -10.04 20.0799
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.83 t_omega_torsion 3.2 t_angle_deg 1.17 t_bond_d 0.01 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 19.83 t_omega_torsion 3.2 t_angle_deg 1.17 t_bond_d 0.01 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 4763 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 20
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PHASER phasing