3CKT

HIV-1 protease in complex with a dimethylallyl decorated pyrrolidine based inhibitor (orthorombic space group)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PQZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52933.5M NaCl, 0.1M BisTris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.12659642.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.018α = 90
b = 57.581β = 90
c = 61.365γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray196CCDMAR CCD 165 mmdouble crystal monochromator with two sets of mirrors2007-06-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.91841BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.652598.80.0520.05226.14.42252615.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.6889.40.350.352.72.5993

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R2PQZ1.6510242127121271111893.90.20180.1850.1830.239RANDOM
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
115541650
RMS Deviations
KeyRefinement Restraint Deviation
s_similar_adp_cmpnt0.063
s_non_zero_chiral_vol0.042
s_zero_chiral_vol0.04
s_from_restr_planes0.0265
s_angle_d0.024
s_anti_bump_dis_restr0.017
s_bond_d0.007
s_similar_dist
s_rigid_bond_adp_cmpnt
s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1483
Nucleic Acid Atoms
Solvent Atoms124
Heterogen Atoms43

Software

Software
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing