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VP16-VP17 complex, a complex of the two major capsid proteins of bacteriophage P23-77
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZMO PDB ENTRIES 3ZMO AND 3ZMN experimental model PDB 3ZMN PDB ENTRIES 3ZMO AND 3ZMN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 SITTING DROP VAPOUR DIFFUSION SYSTEM IN A 96-WELL PLATE, 100 NL OF PROTEIN MIXTURE CONSISTING OF VP16 AND VP17 (1.7 MG/ML AND 2 MG/ML, RESPECTIVELY, IN 20 MM TRIS-BUFFER PH 7.4) MIXED IN 1:1 MOLAR RATIO, WAS MIXED WITH 100 NL SOLUTION CONSISTING OF 1.1 M DIAMMONIUM TARTRATE PH 7. ONE WELL-DIFFRACTING CRYSTAL THAT WAS USED FOR DATA COLLECTION TOOK THREE MONTHS TO GROW.
Crystal Properties Matthews coefficient Solvent content 2.07 40.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.78 α = 90 b = 69.61 β = 104.99 c = 81.62 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 PIXEL DECTRIS PILATUS 6M 2010-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 Diamond I24
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 1.53 39.6 98.4 0.06 17.7 6.3 61458 23.42
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 1.53 1.57 83.3 1.02 2.9 4.4
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 PDB ENTRIES 3ZMO AND 3ZMN 1.53 22.4 61425 3110 98.1 0.173 0.1717 0.1688 0.1974 0.1933 RANDOM 28.93
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] -1.0078 -2.7567 -1.256 2.2638
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.6 t_omega_torsion 4.1 t_angle_deg 1.07 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 14.6 t_omega_torsion 4.1 t_angle_deg 1.07 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 2878 Nucleic Acid Atoms Solvent Atoms 395 Heterogen Atoms 2
Software Software Software Name Purpose BUSTER refinement xia2 data reduction XDS data reduction xia2 data scaling PHASER phasing