☰ Navigation Tabs
Wild Type HIV-1 Protease with Antiviral Drug Saquinavir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NMY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 298 AMMONIUM SULFATE 40%, CITRATE PHOSPHATE BUFFER PH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298 K
Crystal Properties Matthews coefficient Solvent content 2.27 45.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.1 α = 90 b = 59.78 β = 90 c = 62.49 γ = 90
Symmetry Space Group P 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 90 CCD MARMOSAIC 300 mm CCD 2004-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.000 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 1.16 50 96.6 0.075 14.6 5.6 67949 67949 9.946
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 1.16 1.2 72.6 0.348 3 3
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-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 FREE R 2NMY 1.16 10 65534 65534 3279 96.5 0.1392 0.1371 0.1371 0.1461 0.1779 0.1764 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 24 1640.7 1762.9
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.129 s_non_zero_chiral_vol 0.115 s_zero_chiral_vol 0.071 s_angle_d 0.04 s_similar_adp_cmpnt 0.038 s_anti_bump_dis_restr 0.032 s_from_restr_planes 0.0285 s_bond_d 0.017 s_rigid_bond_adp_cmpnt 0.005 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1512 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 65
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing SHELXL-97 refinement HKL-2000 data reduction HKL-2000 data scaling