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VP16, a capsid protein of bacteriophage P23-77 (VP16-type-2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZMO PDB ENTRY 3ZMO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 SITTING DROP VAPOUR DIFFUSION SYSTEM IN A 96-WELL PLATE, 200 NL OF PROTEIN (2-3 MG/ML IN 20 MM TRIS-BUFFER PH 7.4) MIXED WITH 200 NL SOLUTION CONSISTING 20%(W/V) PEG6000 AND 0.1 M CITRATE PH 4.
Crystal Properties Matthews coefficient Solvent content 2.15 39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.6 α = 90 b = 68.57 β = 96.44 c = 31.58 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 CCD 2010-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 1.26 34.3 85.8 0.05 23.1 7.5 37146 10.67
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 1.26 1.3 41.4 0.63 2.6 6.5
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 ENTRY 3ZMO 1.26 17.79 37133 1855 84.96 0.1577 0.1563 0.1555 0.184 0.1837 RANDOM 16.06
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] -1.1331 -0.983 0.3885 0.7446
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 12.68 t_omega_torsion 4.41 t_angle_deg 1.08 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 12.68 t_omega_torsion 4.41 t_angle_deg 1.08 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 1167 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 14
Software Software Software Name Purpose BUSTER refinement xia2 data reduction xia2 data scaling PHASER phasing