1M9C

X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type Complex.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8294PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.0936

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.445α = 90
b = 113.235β = 100.53
c = 67.006γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 41997-07-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X12C1.0NSLSX12C

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
1238830.0630.06314.82.83805731588-3-335.4
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)
22.03600.1950.1952.81.551153

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 REPLACEMENTTHROUGHOUTPDB ENTRY 1AK4237.8-328437312582.950.201280.2010.195060.25934RANDOM29.841
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]
-1.95-0.43.71-1.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg19.12
r_dihedral_angle_1_deg5.066
r_scangle_it3.86
r_mcangle_it3.824
r_scbond_it2.723
r_angle_refined_deg2.704
r_mcbond_it2.687
r_angle_other_deg1.634
r_symmetry_hbond_refined0.256
r_nbd_refined0.219
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg19.12
r_dihedral_angle_1_deg5.066
r_scangle_it3.86
r_mcangle_it3.824
r_scbond_it2.723
r_angle_refined_deg2.704
r_mcbond_it2.687
r_angle_other_deg1.634
r_symmetry_hbond_refined0.256
r_nbd_refined0.219
r_symmetry_vdw_refined0.184
r_xyhbond_nbd_refined0.173
r_chiral_restr0.162
r_nbd_other0.162
r_symmetry_vdw_other0.162
r_symmetry_hbond_other0.141
r_nbtor_other0.031
r_xyhbond_nbd_other0.027
r_bond_refined_d0.018
r_gen_planes_refined0.015
r_gen_planes_other0.007
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4712
Nucleic Acid Atoms
Solvent Atoms144
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
REFMACrefinement
X-PLORphasing