2NXD

Structure of HIV-1 protease D25N complexed with rt-rh analogue peptide GLY-ALA-ASP-ILE-PHE*TYR-LEU-ASP-GLY-ALA


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.2298126 mM sodium phosphate pH 6.2; 63mM sodium citrate; 25-35%Ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthew coefficientSolvent content
238.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.171α = 90
b = 57.692β = 90
c = 61.482γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200IMAGE PLATERIGAKU RAXIS IVYale Mirrors2005-03-29MSINGLE 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
1242.0792.70.0340.03421.251190911909

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 TMC114242.07112951129558692.820.19790.19790.195050.25737RANDOM46.962
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]
-0.82-0.81.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.513
r_dihedral_angle_4_deg16.62
r_dihedral_angle_3_deg14.756
r_dihedral_angle_1_deg7.125
r_scangle_it2.177
r_scbond_it1.514
r_angle_refined_deg1.218
r_mcangle_it0.986
r_mcbond_it0.786
r_angle_other_deg0.678
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.513
r_dihedral_angle_4_deg16.62
r_dihedral_angle_3_deg14.756
r_dihedral_angle_1_deg7.125
r_scangle_it2.177
r_scbond_it1.514
r_angle_refined_deg1.218
r_mcangle_it0.986
r_mcbond_it0.786
r_angle_other_deg0.678
r_symmetry_vdw_other0.198
r_nbd_other0.19
r_nbd_refined0.188
r_nbtor_refined0.171
r_xyhbond_nbd_refined0.167
r_mcbond_other0.163
r_symmetry_vdw_refined0.15
r_symmetry_hbond_refined0.144
r_nbtor_other0.081
r_chiral_restr0.072
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.004
r_gen_planes_other0.001
r_symmetry_metal_ion_other
r_sphericity_bonded
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_rigid_bond_restr
r_sphericity_free
r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1540
Nucleic Acid Atoms
Solvent Atoms74
Heterogen Atoms

Software

Software
Software NamePurpose
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling