1SP5

Crystal structure of HIV-1 protease complexed with a product of autoproteolysis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1A30PDB ENTRY 1A30

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5279sodium chloride 0.8-0.9M, sodium citrate 50mM, DMSO 5%, sodium acetate 5mM, EDTA 0.5mM, DTT 0.25mM, Boc-Phe-psi[(S)-CH(OH)CH2NH]Phe-Ile-Phe-NH2 270mM, protein 3mg/ml in drop, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Crystal Properties
Matthews coefficientSolvent content
2.3747.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.765α = 90
b = 86.284β = 90
c = 45.834γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2000-07-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2R1.0ELETTRA5.2R

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
11.8012596.70.0490.04930.84.3211522115214
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)
1.81.8392.90.2320.23273.8988

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1A301.819.12112921129102396.70.1780.1780.1770.211RANDOM15.9
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]
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d26.2
c_scangle_it4.57
c_scbond_it3.03
c_mcangle_it2.33
c_angle_deg1.6
c_mcbond_it1.55
c_improper_angle_d0.92
c_bond_d0.013
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d26.2
c_scangle_it4.57
c_scbond_it3.03
c_mcangle_it2.33
c_angle_deg1.6
c_mcbond_it1.55
c_improper_angle_d0.92
c_bond_d0.013
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1567
Nucleic Acid Atoms
Solvent Atoms135
Heterogen Atoms19

Software

Software
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing