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Crystal structure of HIV-1 Reverse Transcriptase RNase H domain complexed with a galloyl inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8JYH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 291 0.1M MES, 26%(v/v) PEG 6000, 0.01M Zinc Sulfate, 0.001M MANGANESE CHLORIDE
Crystal Properties Matthews coefficient Solvent content 2.32 46.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.255 α = 90 b = 61.255 β = 90 c = 83.122 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 PIXEL DECTRIS EIGER X 4M 2024-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.96 43.31 100 0.082 0.084 0.017 0.999 24 24.1 11986
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.96 2.01 100 1.322 1.349 0.264 0.88 25.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.96 43.31 1.33 11512 1151 96.42 0.2537 0.2505 0.2584 0.2816 0.2906
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.394 f_angle_d 1.078 f_chiral_restr 0.041 f_bond_d 0.007 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1154 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms 33
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing