4R5P

Crystal structure of HIV-1 reverse transcriptase (RT) with DNA and a nucleoside triphosphate mimic alpha-carboxy nucleoside phosphonate inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3V4IPDB ENTRY 3V4I

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.227710% PEG8000, 100 mM ammonium sulfate, 5% w/v sucrose, 5% w/v glycerol, 20 mM magnesium chloride, 50 mM Bis-Tris propane, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.2462.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.905α = 90
b = 133.529β = 97.81
c = 139.218γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702013-10-13MSINGLE 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
12.8945099.60.1078.947242072131-1
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)
12.8942.9599.20.6341.853.43540

Refinement

Statistics
Diffraction IDStructure Solution 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 REPLACEMENTPDB ENTRY 3V4I2.89444.5367242072084215199.220.19650.19650.19490.2506RANDOM
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
f_dihedral_angle_d20.022
f_angle_d1.514
f_chiral_restr0.112
f_bond_d0.012
f_plane_restr0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15801
Nucleic Acid Atoms1804
Solvent Atoms6
Heterogen Atoms103

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling