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Crystal structure of HIV-1 RNase H p15 with engineered E. coli loop and active site inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HRH PDB code 1HRH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 1.0M MgSO4, 100mM sodium acetate pH 4.6, 5mM manganese chloride, 5mM TCEP, 1.5mM inhibitor, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3 59.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.717 α = 90 b = 90.326 β = 90 c = 113.334 γ = 90
Symmetry Space Group I 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 210 2008-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1.0 ALS 5.0.1
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 1.6 29.1 97.7 0.048 37.5 5.3 26856 26856 17.8
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 1.6 1.63 76.4 0.347 2.9 3.8 1019
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 PDB code 1HRH 1.7 29.1 22881 22030 1050 96.1 0.198 0.196 0.2078 0.232 0.246 RANDOM 30.3
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] 8.19 -6.18 -2.01
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.4 c_scangle_it 11.21 c_scbond_it 9.93 c_mcangle_it 7.15 c_mcbond_it 5.54 c_angle_deg 0.9 c_improper_angle_d 0.62 c_bond_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1135 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 38
Software Software Software Name Purpose BOS data collection AMoRE phasing CNX refinement HKL-2000 data reduction HKL-2000 data scaling