3LAM

Crystal structure of HIV-1 reverse transcriptase in complex with N1-propyl pyrimidinedione non-nucleoside inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VRTpdb entry 1VRT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52931.3M ammonium sulfate, 100mM cacodylate, 5mM sodium malonate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7555.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.641α = 90
b = 154.473β = 90
c = 153.812γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-03-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21.0ALS5.0.2

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
12.755099.70.05422.84.83645757.5
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)
2.752.81000.5053.14.7

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1VRT2.7629.913640334539171693.30.2340.2310.28RANDOM70.5
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]
-2.62-3.666.27
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.4
c_scangle_it3.17
c_mcangle_it2.83
c_scbond_it1.96
c_improper_angle_d1.81
c_angle_deg1.7
c_mcbond_it1.61
c_bond_d0.141
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.4
c_scangle_it3.17
c_mcangle_it2.83
c_scbond_it1.96
c_improper_angle_d1.81
c_angle_deg1.7
c_mcbond_it1.61
c_bond_d0.141
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7842
Nucleic Acid Atoms
Solvent Atoms103
Heterogen Atoms50

Software

Software
Software NamePurpose
BOSdata collection
EPMRphasing
CNXrefinement
HKL-2000data reduction
HKL-2000data scaling