☰ Navigation Tabs
Human foamy virus integrase - catalytic core. Manganese-bound structure.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X74 PDB ENTRY 2X74
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 1.8-2M AMMONIUM FORMATE 100MM HEPES, PH 7.5 5MM MNCL2 10-15% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.64 53.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.767 α = 90 b = 89.232 β = 90 c = 177.084 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 180 CCD ADSC QUANTUM 315r KB-MIRRORS 2009-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 SOLEIL PROXIMA 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 2.06 49.23 93.8 0.07 14.2 3.5 78830 32.52
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 2.06 2.17 71 0.7 2 2.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2X74 2.06 44.62 74893 3937 93.47 0.22793 0.22574 0.27004 0.2439 RANDOM 44.994
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] 2.1 -1.73 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.856 r_dihedral_angle_3_deg 16.985 r_dihedral_angle_4_deg 13.927 r_dihedral_angle_1_deg 5.175 r_scangle_it 2.475 r_mcangle_it 1.719 r_scbond_it 1.589 r_angle_refined_deg 1.085 r_mcbond_it 0.955 r_chiral_restr 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.856 r_dihedral_angle_3_deg 16.985 r_dihedral_angle_4_deg 13.927 r_dihedral_angle_1_deg 5.175 r_scangle_it 2.475 r_mcangle_it 1.719 r_scbond_it 1.589 r_angle_refined_deg 1.085 r_mcbond_it 0.955 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 8708 Nucleic Acid Atoms Solvent Atoms 314 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing