2Q64

HIV-1 PR mutant in complex with nelfinavir


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1U8G 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.4298reservoir solution: 0.5M (NH4)2SO4, 0.1M MES pH 5.4 or pH 5.5; drops: 2+1ul (protein+reservoir}; protein: 3-5mg/ml 5-fold molar excess of inhibitor, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1442.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.168α = 90
b = 62.168β = 90
c = 82.179γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmdouble crystal monochromator2005-02-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM160.98ESRFBM16

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
12.5501000.09776313-349.9
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)
12.52.61000.4221.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1U8G2.53059753021000.18280.179240.25772RANDOM46.728
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]
0.340.170.34-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.873
r_dihedral_angle_4_deg19.15
r_dihedral_angle_3_deg17.047
r_dihedral_angle_1_deg6.832
r_scangle_it1.912
r_angle_refined_deg1.431
r_scbond_it1.142
r_mcangle_it0.892
r_mcbond_it0.532
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.873
r_dihedral_angle_4_deg19.15
r_dihedral_angle_3_deg17.047
r_dihedral_angle_1_deg6.832
r_scangle_it1.912
r_angle_refined_deg1.431
r_scbond_it1.142
r_mcangle_it0.892
r_mcbond_it0.532
r_nbtor_refined0.306
r_nbd_refined0.202
r_symmetry_vdw_refined0.2
r_symmetry_hbond_refined0.195
r_xyhbond_nbd_refined0.122
r_chiral_restr0.09
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1504
Nucleic Acid Atoms
Solvent Atoms55
Heterogen Atoms40

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling