1M9E | pdb_00001m9e

X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type H87A Complex.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AK4PDB entry 1AK4

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
2.0736

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.289α = 90
b = 110.989β = 101.02
c = 67.685γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 41998-04-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL1-51.07SSRLBL1-5

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
11.7226780.0560.0569.44.65262441047-3-330.3
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)
1.721.82310.3040.3042.32.71721

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1AK41.7225.73-35262441047462377.70.178110.1780.172860.180.225710.23RANDOM20.181
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]
-0.67-0.351.29-0.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg19.417
r_dihedral_angle_1_deg6.081
r_scangle_it4.76
r_mcangle_it3.998
r_scbond_it3.195
r_angle_refined_deg3.034
r_mcbond_it2.875
r_angle_other_deg1.218
r_symmetry_vdw_refined0.3
r_symmetry_vdw_other0.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg19.417
r_dihedral_angle_1_deg6.081
r_scangle_it4.76
r_mcangle_it3.998
r_scbond_it3.195
r_angle_refined_deg3.034
r_mcbond_it2.875
r_angle_other_deg1.218
r_symmetry_vdw_refined0.3
r_symmetry_vdw_other0.26
r_nbd_refined0.241
r_symmetry_hbond_refined0.229
r_nbd_other0.214
r_xyhbond_nbd_refined0.186
r_chiral_restr0.181
r_xyhbond_nbd_other0.068
r_bond_refined_d0.018
r_gen_planes_refined0.017
r_gen_planes_other0.008
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4677
Nucleic Acid Atoms
Solvent Atoms380
Heterogen Atoms

Software

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