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Cyclic hexapeptide PKIDNG in complex with HIV-1 integrase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3L3U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 1.8M AMMONIUM SULFATE, 0.15M SODIUM CITRATE, 5mM CADMIUM CHLORIDE , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.07 40.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.68 α = 90 b = 49.68 β = 90 c = 102.93 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 315r Mirrors 2009-08-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.954 Australian Synchrotron MX2
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 1.7 39.7 99.1 0.06 29655 29394 166415
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.8 86.6 0.377 0.459 4.2 5.6 4235
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 (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 3L3U 1.7 39.7 31259 29394 1547 100 0.19667 0.19503 0.1986 0.22775 0.2364 RANDOM 24.598
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] 1.28 0.64 1.28 -1.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.502 r_dihedral_angle_4_deg 15.719 r_dihedral_angle_3_deg 15.211 r_dihedral_angle_1_deg 6.13 r_scangle_it 5.597 r_angle_other_deg 4.21 r_scbond_it 3.464 r_mcangle_it 2.683 r_angle_refined_deg 1.855 r_mcbond_it 1.597
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.502 r_dihedral_angle_4_deg 15.719 r_dihedral_angle_3_deg 15.211 r_dihedral_angle_1_deg 6.13 r_scangle_it 5.597 r_angle_other_deg 4.21 r_scbond_it 3.464 r_mcangle_it 2.683 r_angle_refined_deg 1.855 r_mcbond_it 1.597 r_chiral_restr 0.117 r_bond_refined_d 0.023 r_gen_planes_other 0.013 r_gen_planes_refined 0.009 r_bond_other_d 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 2159 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 36
Software Software Software Name Purpose Blu-Ice data collection AMoRE phasing REFMAC refinement XDS data reduction XDS data scaling