3D1X

Crystal structure of HIV-1 mutant I54M and inhibitor saquinavir


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DAZPDB entry 1DAZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5295SODIUM ACETATE BUFFER, 10-15% NaCl, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.7354.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.9α = 90
b = 86.02β = 90
c = 46.39γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDMARMOSAIC 300 mm CCD2007-06-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-IDAPS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.055092.20.08821.96.61031729518442
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.051.0993.50.25874.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE RPDB entry 1DAZ1.051010317295184516493.50.15470.1190.147RANDOM
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 MethodRefinement High ResolutionRefinement Low Resolution
3415901785.8
RMS Deviations
KeyRefinement Restraint Deviation
s_non_zero_chiral_vol0.108
s_zero_chiral_vol0.094
s_approx_iso_adps0.094
s_anti_bump_dis_restr0.046
s_similar_adp_cmpnt0.038
s_angle_d0.036
s_from_restr_planes0.0313
s_bond_d0.017
s_rigid_bond_adp_cmpnt0.006
s_similar_dist
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1512
Nucleic Acid Atoms
Solvent Atoms250
Heterogen Atoms58

Software

Software
Software NamePurpose
AMoREphasing
SHELXL-97refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling