3BO7 | pdb_00003bo7

Crystal structure of Toxoplasma gondii peptidyl-prolyl cis-trans isomerase, 541.m00136


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FU0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.328% PEG 3350, 0.2 M LISO4, 0.1 M HEPES PH 7.3, 2 MM TCEP, 2 MM CYCLOSPORIN A, 20% ETHYLENE GLYCOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
Crystal Properties
Matthews coefficientSolvent content
2.9858.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 149.631α = 90
b = 100.805β = 116.28
c = 86.184γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2007-10-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ DW

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
12.255099.90.1240.0836.93.75446644.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.252.3399.90.8341.33.6

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2FUO2.3533.5447813242299.90.1920.190.190.2450.24RANDOM39.21
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]
0.12-0.07-0.310.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.596
r_dihedral_angle_4_deg19.088
r_dihedral_angle_3_deg15.687
r_dihedral_angle_1_deg5.712
r_scangle_it1.929
r_angle_refined_deg1.2
r_scbond_it1.166
r_mcangle_it0.879
r_mcbond_it0.505
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.596
r_dihedral_angle_4_deg19.088
r_dihedral_angle_3_deg15.687
r_dihedral_angle_1_deg5.712
r_scangle_it1.929
r_angle_refined_deg1.2
r_scbond_it1.166
r_mcangle_it0.879
r_mcbond_it0.505
r_nbtor_refined0.311
r_nbd_refined0.199
r_symmetry_vdw_refined0.141
r_xyhbond_nbd_refined0.13
r_symmetry_hbond_refined0.082
r_chiral_restr0.079
r_bond_refined_d0.009
r_gen_planes_refined0.004
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 Atoms5676
Nucleic Acid Atoms
Solvent Atoms484
Heterogen Atoms138

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling