2POY | pdb_00002poy

Cryptosporidium parvum cyclophilin type peptidyl-prolyl cis-trans isomerase cgd2_4120 in complex with cyclosporin A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PLUPDB ENTRY 2PLU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
13.525 % PEG 3350, 0.1 M CITRIC ACID PH 3.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties
Matthews coefficientSolvent content
2.1542.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.482α = 90
b = 119.303β = 90
c = 127.877γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102007-04-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE F1CHESSF1

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
11.85097.40.1030.0836.76.851177
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)
11.81.8678.80.3530.3122.44.1

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 2PLU1.834.8851164259897.30.1950.1930.190.2330.23RANDOM21.33
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]
-0.250.43-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.327
r_dihedral_angle_3_deg13.486
r_dihedral_angle_4_deg11.433
r_dihedral_angle_1_deg6.452
r_scangle_it3.36
r_scbond_it2.225
r_angle_refined_deg1.536
r_mcangle_it1.472
r_mcbond_it0.916
r_nbtor_refined0.319
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.327
r_dihedral_angle_3_deg13.486
r_dihedral_angle_4_deg11.433
r_dihedral_angle_1_deg6.452
r_scangle_it3.36
r_scbond_it2.225
r_angle_refined_deg1.536
r_mcangle_it1.472
r_mcbond_it0.916
r_nbtor_refined0.319
r_nbd_refined0.222
r_symmetry_vdw_refined0.18
r_xyhbond_nbd_refined0.132
r_symmetry_hbond_refined0.13
r_chiral_restr0.104
r_bond_refined_d0.015
r_gen_planes_refined0.006
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 Atoms4096
Nucleic Acid Atoms
Solvent Atoms315
Heterogen Atoms

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling