4B3Q

Structures of HIV-1 RT and RNA-DNA Complex Reveal a Unique RT Conformation and Substrate Interface


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RTDPDB ENTRIES 1RTD, 1FK9
experimental modelPDB 1FK9PDB ENTRIES 1RTD, 1FK9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.5277RT COMPLEX WAS MIXED WITH RESERVOIR SOLUTION CONTAINING 1.8M (NH4)2SO4, 50MM TRIS HCL (PH8.5), AND 25MM MGSO4. VAPOR DIFFUSION 4C.
Crystal Properties
Matthews coefficientSolvent content
682

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 272.7α = 90
b = 272.7β = 90
c = 233.1γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH MAR300ADJUSTABLE FOCUS K-B PAIR SI MIRRORS2011-07-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-BAPS23-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
156099.60.1414.86.5146462170.34
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
155.091000.871.76.8

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRIES 1RTD, 1FK9529.98711300566289.810.36320.3610.4073149
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_d13.78
f_angle_d0.802
f_chiral_restr0.054
f_bond_d0.008
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7535
Nucleic Acid Atoms878
Solvent Atoms
Heterogen Atoms20

Software

Software
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing