3V81

Crystal structure of HIV-1 reverse transcriptase (RT) with DNA and the nonnucleoside inhibitor nevirapine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3V6DPDB ENTRY 3V6D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.8277PEG 8000, ammonium sulfate, sucrose, glycerol, magnesium chloride, Bis-Tris propane , pH 6.8, VAPOR DIFFUSION, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.2261.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.822α = 90
b = 132.052β = 100.84
c = 142.732γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 270mirror2011-03-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE F10.918CHESSF1

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
12.8540990.0910.13.675389-1
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)
12.852.997.70.6182.93706

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 3V6D2.850338.41375359228798.680.2520.25050.29882.9103
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]
-2.12612.70785.1163-2.9902
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d18.556
f_angle_d1.337
f_chiral_restr0.091
f_bond_d0.01
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15824
Nucleic Acid Atoms1646
Solvent Atoms
Heterogen Atoms40

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOLREPphasing