3BKP

Crystal structure of the Toxoplasma gondii cyclophilin, 49.m03261


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HQ6PDB entry 2HQ6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529325% PEG 3350, 0.2M NaCl, 0.1M Hepes pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0239.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.358α = 90
b = 63.302β = 90
c = 63.528γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2007-09-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ DW1.5418

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
11.85099.60.0840.05110.16.9201312013121.3
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)
11.81.8698.30.6560.5893.266.81960

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 2HQ61.844.862008320083102299.540.1670.1640.219RANDOM21.209
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]
0.6-0.650.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.001
r_dihedral_angle_4_deg25.002
r_dihedral_angle_3_deg12.17
r_dihedral_angle_1_deg6.279
r_scangle_it5.817
r_scbond_it3.804
r_mcangle_it2.495
r_angle_refined_deg2.333
r_mcbond_it1.702
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.001
r_dihedral_angle_4_deg25.002
r_dihedral_angle_3_deg12.17
r_dihedral_angle_1_deg6.279
r_scangle_it5.817
r_scbond_it3.804
r_mcangle_it2.495
r_angle_refined_deg2.333
r_mcbond_it1.702
r_nbtor_refined0.311
r_nbd_refined0.226
r_symmetry_vdw_refined0.213
r_chiral_restr0.18
r_xyhbond_nbd_refined0.164
r_symmetry_hbond_refined0.156
r_bond_refined_d0.032
r_gen_planes_refined0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1418
Nucleic Acid Atoms
Solvent Atoms191
Heterogen Atoms24

Software

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