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Crystal structure of HPV6a E2 DNA binding domain bound to an 18 base pair DNA target
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JJ4 PDB Entry 1JJ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 sodium chloride, Hepes, ammonium sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.7 54.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.449 α = 90 b = 73.449 β = 90 c = 109.237 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 CCD ADSC QUANTUM 4 mirrors 2005-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.1 1.488 SRS PX14.1
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 3.1 63.63 99.9 0.118 17.9 7.6 5807 6087 2 2
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) 3.1 3.18 99.8 0.351 4.2 7.1 429
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1JJ4 3.1 63.63 5807 6085 278 99.85 0.206 0.247 0.203 0.2005 0.288 0.2838 RANDOM 64.548
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] 4.17 2.08 4.17 -6.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.469 r_dihedral_angle_4_deg 22.469 r_dihedral_angle_3_deg 22.032 r_dihedral_angle_1_deg 12 r_angle_refined_deg 2.322 r_scangle_it 2.085 r_mcangle_it 1.376 r_scbond_it 1.203 r_mcbond_it 0.744 r_nbtor_refined 0.325
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.469 r_dihedral_angle_4_deg 22.469 r_dihedral_angle_3_deg 22.032 r_dihedral_angle_1_deg 12 r_angle_refined_deg 2.322 r_scangle_it 2.085 r_mcangle_it 1.376 r_scbond_it 1.203 r_mcbond_it 0.744 r_nbtor_refined 0.325 r_nbd_refined 0.278 r_chiral_restr 0.26 r_symmetry_vdw_refined 0.227 r_xyhbond_nbd_refined 0.163 r_symmetry_hbond_refined 0.029 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1444 Nucleic Acid Atoms 732 Solvent Atoms 19 Heterogen Atoms
Software Software Software Name Purpose PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction SCALEPACK data scaling