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Structure of the arm-type binding domain of HPI integrase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 277 0.1M tri-sodium citrate, pH5.6, 35% tert-butanol, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.18 43.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.75 α = 90 b = 48.75 β = 90 c = 74.2 γ = 90
Symmetry Space Group P 41 21 2
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 MARMOSAIC 225 mm CCD mirror 2009-03-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9873 SLS X10SA
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 1.3 10 85 0.036 29.07 22769 19463 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) 1 1.3 1.4 65.5 0.103 8.98
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 1.3 10 2 22769 18404 963 85.35 0.2138 0.2125 0.2051 0.23867 0.2321 RANDOM 16.726
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] -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.389 r_dihedral_angle_4_deg 16.942 r_dihedral_angle_3_deg 10.596 r_dihedral_angle_1_deg 5.692 r_scangle_it 3.442 r_scbond_it 2.151 r_mcangle_it 1.546 r_angle_refined_deg 1.28 r_mcbond_it 0.805 r_chiral_restr 0.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.389 r_dihedral_angle_4_deg 16.942 r_dihedral_angle_3_deg 10.596 r_dihedral_angle_1_deg 5.692 r_scangle_it 3.442 r_scbond_it 2.151 r_mcangle_it 1.546 r_angle_refined_deg 1.28 r_mcbond_it 0.805 r_chiral_restr 0.079 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 604 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 1
Software Software Software Name Purpose MAR345 data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling