3LRY

Crystal structure of synthetic HIV-1 capsid C-terminal domain (CCA)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52980.1 M HEPES, 0.8 M potassium phosphate monohydrate, 0.8M potassium phosphate monobasic, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthew coefficientSolvent content
2.7354.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.907α = 90
b = 58.932β = 133.45
c = 58.732γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2009-02-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.9842.636960.0650.06814.53144221381911
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.982.0195.60.5780.50722.8695

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 1A431.9820118341245862495.930.2160.2130.269RANDOM38.421
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]
3.623.56-2.223.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.828
r_dihedral_angle_4_deg22.282
r_dihedral_angle_3_deg15.266
r_dihedral_angle_1_deg5.833
r_scangle_it5.011
r_scbond_it2.948
r_mcangle_it1.642
r_angle_refined_deg1.593
r_mcbond_it0.926
r_chiral_restr0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.828
r_dihedral_angle_4_deg22.282
r_dihedral_angle_3_deg15.266
r_dihedral_angle_1_deg5.833
r_scangle_it5.011
r_scbond_it2.948
r_mcangle_it1.642
r_angle_refined_deg1.593
r_mcbond_it0.926
r_chiral_restr0.11
r_bond_refined_d0.019
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1130
Nucleic Acid Atoms
Solvent Atoms85
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing