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HIV-1 REVERSE TRANSCRIPTASE COMPLEX WITH DNA AND D-ASPARTATE TENOFOVIR WITH BOUND MANGANESE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3V4I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 16-19.5% v/v PEG Smear Broad,
0.2 M (NH4)2SO4,
0.1 M Tris-HCl
Crystal Properties Matthews coefficient Solvent content 3.19 61.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.416 α = 90 b = 132.371 β = 98.48 c = 138.744 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS 6M 2018-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9763 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.73 69.8 99.7 0.1 0.064 0.991 7.3 3.4 84580 58.55
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.73 2.78 99.5 0.388 0.254 0.286 2.7 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3V4I 2.73 69.8 1.46 84547 2529 99.58 0.2153 0.2141 0.2144 0.2536 0.2538 77.03
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 15.2973 f_angle_d 0.4429 f_chiral_restr 0.0395 f_plane_restr 0.0029 f_bond_d 0.0021
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15835 Nucleic Acid Atoms 1778 Solvent Atoms 108 Heterogen Atoms 58
Software Software Software Name Purpose PHENIX refinement MxCuBE data collection MOSFLM data reduction Aimless data scaling PHENIX phasing Coot model building