2NXL

Structure of HIV-1 protease D25N complexed with the rt-rh analogue peptide GLY-ALA-GLU-VAL-PHE*TYR-VAL-ASP-GLY-ALA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1T3R1T3R = Crystal structure of HIV- 1 protease complexed with the inhibitor TMC114

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.2298126 mM sodium phosphate pH 6.2; 63mM sodium citrate; 25-35% Ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
238.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.861α = 90
b = 57.5β = 90
c = 61.887γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200IMAGE PLATERIGAKU RAXIS IVYale mirrors2005-03-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
1242.1195.80.0710.07112.551233212332

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1T3R = Crystal structure of HIV- 1 protease complexed with the inhibitor TMC114242.11116931169360895.920.163070.163070.160350.216RANDOM37.719
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]
1.080.01-1.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.41
r_dihedral_angle_3_deg13.77
r_dihedral_angle_4_deg12.352
r_dihedral_angle_1_deg6.659
r_scangle_it2.1
r_angle_refined_deg1.455
r_scbond_it1.411
r_mcangle_it0.897
r_angle_other_deg0.781
r_mcbond_it0.723
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.41
r_dihedral_angle_3_deg13.77
r_dihedral_angle_4_deg12.352
r_dihedral_angle_1_deg6.659
r_scangle_it2.1
r_angle_refined_deg1.455
r_scbond_it1.411
r_mcangle_it0.897
r_angle_other_deg0.781
r_mcbond_it0.723
r_symmetry_vdw_other0.206
r_nbd_refined0.198
r_nbd_other0.184
r_nbtor_refined0.17
r_symmetry_vdw_refined0.169
r_symmetry_hbond_refined0.16
r_mcbond_other0.152
r_xyhbond_nbd_refined0.133
r_chiral_restr0.087
r_nbtor_other0.084
r_symmetry_hbond_other0.05
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1565
Nucleic Acid Atoms
Solvent Atoms137
Heterogen Atoms10

Software

Software
Software NamePurpose
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling