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HIV-1 IN core domain in complex with 4-(1H-pyrrol-1-yl)aniline
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3L3U PDB ENTRY 3l3u
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 295 1.6M AmSO4, 0.1M Na Citrate pH 5.6, 50mM CdCl2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.21 44.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.284 α = 90 b = 61.658 β = 90 c = 82.017 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 ADSC QUANTUM 210r Mirror 2007-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.95363 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.6 34.15 99.57 0.08 0.09 15.2 7.2 38588 38422 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.634 1.692 95.74
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 3l3u 1.63 34.15 38588 36498 1924 99.46 0.199 0.20042 0.199 0.2058 0.22677 0.2323 RANDOM 20.482
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] -0.33 1.43 -1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.937 r_dihedral_angle_3_deg 14.657 r_dihedral_angle_4_deg 13.073 r_dihedral_angle_1_deg 5.987 r_scangle_it 3.293 r_scbond_it 2.293 r_angle_refined_deg 1.749 r_mcangle_it 1.715 r_mcbond_it 1.202 r_angle_other_deg 0.959
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.937 r_dihedral_angle_3_deg 14.657 r_dihedral_angle_4_deg 13.073 r_dihedral_angle_1_deg 5.987 r_scangle_it 3.293 r_scbond_it 2.293 r_angle_refined_deg 1.749 r_mcangle_it 1.715 r_mcbond_it 1.202 r_angle_other_deg 0.959 r_symmetry_vdw_other 0.29 r_mcbond_other 0.241 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.2 r_nbd_other 0.199 r_metal_ion_refined 0.19 r_symmetry_hbond_refined 0.181 r_symmetry_vdw_refined 0.177 r_nbtor_refined 0.176 r_chiral_restr 0.086 r_nbtor_other 0.083 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2190 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms 61
Software Software Software Name Purpose Blu-Ice data collection AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling