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Crystal structure analysis of HIV-1 protease with a substrate analog P1-P6
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 10%, DMSO 5%,SODIUM ACETATE BUFFER, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.61 52.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.91 α = 90 b = 86.069 β = 90 c = 46.542 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 MARRESEARCH 2002-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.99997 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 1.4 50 88.3 0.074 47418
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 1.4 1.45 96.5 0.19
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 PDB Entry 1DAZ 1.4 10 42720 40185 2258 95.2 0.154 0.1585 0.1612 0.1692 0.2096 0.2165 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 52 1664.2 1776.07
RMS Deviations Key Refinement Restraint Deviation s_non_zero_chiral_vol 0.08 s_approx_iso_adps 0.077 s_zero_chiral_vol 0.076 s_similar_adp_cmpnt 0.051 s_from_restr_planes 0.0361 s_angle_d 0.03 s_anti_bump_dis_restr 0.028 s_bond_d 0.01 s_rigid_bond_adp_cmpnt 0.004 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1594 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 5
Software Software Software Name Purpose MAR345 data collection HKL-2000 data reduction SHELX model building SHELXL-97 refinement HKL-2000 data scaling AMoRE phasing