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Cystal structure of HIV-1 Active Site Mutant D25N and p2-NC analog inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DAZ PDB entry 1DAZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 295 10% SODIUM CHLORIDE, CITRATE-PHOSPHATE BUFFER, 7-8% DMSO, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.63 54.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.196 α = 90 b = 85.893 β = 90 c = 46.547 γ = 90
Symmetry Space Group P 21 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 95 CCD MARRESEARCH 2000-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
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 1.05 50 94.6 0.136 22.3 7 102685 97551 4 2
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 1.05 1.09 82.1 0.35 2.7 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION AB INITIO FREE R PDB entry 1DAZ 1.05 10 2 102685 97551 5134 94 0.1548 0.15 0.18 0.1643 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 37 1663.41 1775.83
RMS Deviations Key Refinement Restraint Deviation s_non_zero_chiral_vol 0.114 s_approx_iso_adps 0.096 s_zero_chiral_vol 0.092 s_anti_bump_dis_restr 0.062 s_similar_adp_cmpnt 0.058 s_angle_d 0.04 s_from_restr_planes 0.0309 s_bond_d 0.017 s_rigid_bond_adp_cmpnt 0.006 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1512 Nucleic Acid Atoms Solvent Atoms 234 Heterogen Atoms 72
Software Software Software Name Purpose SHELX model building SHELXL-97 refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing