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Crystal structure analysis of HIV-1 Protease mutant V82A with a substrate analog P6-PR
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 5 293 AMMONIUM SULFATE 30%, DMSO 7%,SODIUM ACETATE BUFFER, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.61 52.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.882 α = 90 b = 86.283 β = 90 c = 46.404 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 90 CCD ADSC QUANTUM 315 2002-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C 0.97900 NSLS X26C
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 1.42 50 90.3 0.098 17.1 5.1 45584
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 1.42 1.47 100 0.708 2.63 4.9
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R PDB ENTRY 1DAZ 1.42 10 40847 34360 2043 90.3 0.1818 0.1788 0.166 0.2328 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 18 1788.1
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.087 s_non_zero_chiral_vol 0.077 s_zero_chiral_vol 0.067 s_similar_adp_cmpnt 0.037 s_from_restr_planes 0.0342 s_angle_d 0.031 s_anti_bump_dis_restr 0.015 s_bond_d 0.011 s_rigid_bond_adp_cmpnt 0.003 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1586 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 3
Software Software Software Name Purpose HKL-2000 data collection HKL-2000 data reduction SHELX model building SHELXL-97 refinement MAR345 data collection HKL-2000 data scaling AMoRE phasing