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Extended E2 DNA-binding domain of the Bovine Papillomavirus-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BOP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 291 sodium citrate, PEG 4000 and ammonium acetate
Crystal Properties Matthews coefficient Solvent content 1.93 36.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.203 α = 90 b = 55.203 β = 90 c = 203.091 γ = 120
Symmetry Space Group P 31 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 IMAGE PLATE MAR scanner 345 mm plate 2000-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.39 LNLS D03B-MX1
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 1.9 67.8 99.8 0.12 0.045 0.998 10.2 5.1 29354
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 99.3 0.419 0.543
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 2BOP 1.9 67.79 29287 1457 99.89 0.2161 0.2138 0.2202 0.2605 0.2655 RANDOM 28.8264
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] -0.28 -0.14 -0.28 0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.539 r_dihedral_angle_4_deg 16.368 r_dihedral_angle_3_deg 15.393 r_dihedral_angle_1_deg 6.989 r_mcangle_it 3.898 r_angle_other_deg 3.748 r_mcbond_it 2.509 r_mcbond_other 2.508 r_angle_refined_deg 1.763 r_chiral_restr 0.108
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.539 r_dihedral_angle_4_deg 16.368 r_dihedral_angle_3_deg 15.393 r_dihedral_angle_1_deg 6.989 r_mcangle_it 3.898 r_angle_other_deg 3.748 r_mcbond_it 2.509 r_mcbond_other 2.508 r_angle_refined_deg 1.763 r_chiral_restr 0.108 r_bond_refined_d 0.016 r_gen_planes_other 0.012 r_gen_planes_refined 0.01 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2921 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHASER phasing