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Crystal structure of papillomavirus E1 hexameric helicase DNA-free form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GXA PDB ENTRY 2GXA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 K-PHOSPHATE PH 7.5, NACL, PEG3350, MES PH 7.5
Crystal Properties Matthews coefficient Solvent content 2.8 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.111 α = 90 b = 180.649 β = 90 c = 187.533 γ = 90
Symmetry Space Group P 21 21 21
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 MARRESEARCH 2004-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 25 94 0.11 13.5 4.8 86088 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 3 3.11 73 0.51 2.4 3.5
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 2GXA 3 24.95 85189 853 93.4 0.219 0.219 0.2163 0.271 0.2681 RANDOM 77.51
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] 6.93 -4.97 -1.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.948 r_dihedral_angle_3_deg 19.969 r_dihedral_angle_4_deg 17.986 r_dihedral_angle_1_deg 5.598 r_scangle_it 2.731 r_scbond_it 1.559 r_angle_refined_deg 1.185 r_mcangle_it 1.01 r_mcbond_it 0.512 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.948 r_dihedral_angle_3_deg 19.969 r_dihedral_angle_4_deg 17.986 r_dihedral_angle_1_deg 5.598 r_scangle_it 2.731 r_scbond_it 1.559 r_angle_refined_deg 1.185 r_mcangle_it 1.01 r_mcbond_it 0.512 r_nbtor_refined 0.314 r_symmetry_vdw_refined 0.232 r_nbd_refined 0.22 r_xyhbond_nbd_refined 0.145 r_symmetry_hbond_refined 0.139 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25948 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing