3DS5

HIV-1 capsid C-terminal domain mutant (N183A)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION4.629830% PEG 4000, 100mM ammonium acetate, 10mM MgCl2, pH 4.6, EVAPORATION, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.7555.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.359α = 109.2
b = 51.321β = 109.63
c = 51.358γ = 109.55
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDDynamically bendable mirror2007-05-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.044SLSX06SA

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
12.44286.30.0250.02536.43.11357161.8
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)
2.42.4943.60.1390.13952.2692

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 1A802.441.961289267785.940.222690.220150.26977RANDOM60.251
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]
1.680.780.77-0.81-1.57-0.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.755
r_dihedral_angle_4_deg23.891
r_dihedral_angle_3_deg20.618
r_dihedral_angle_1_deg6.339
r_scangle_it3.761
r_scbond_it2.301
r_angle_refined_deg1.617
r_mcangle_it1.427
r_mcbond_it0.809
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.755
r_dihedral_angle_4_deg23.891
r_dihedral_angle_3_deg20.618
r_dihedral_angle_1_deg6.339
r_scangle_it3.761
r_scbond_it2.301
r_angle_refined_deg1.617
r_mcangle_it1.427
r_mcbond_it0.809
r_nbtor_refined0.299
r_symmetry_vdw_refined0.244
r_nbd_refined0.227
r_symmetry_hbond_refined0.21
r_xyhbond_nbd_refined0.136
r_chiral_restr0.092
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2292
Nucleic Acid Atoms
Solvent Atoms22
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
RemDAqdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing