2QER

Crystal structure of Cryptosporidium parvum cyclophilin type peptidyl-prolyl cis-trans isomerase cgd2_1660 in the presence of dipeptide ala-pro


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2POEPDB entry 2POE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529325% PEG 3350, 0.1 M Ammonium sulfate, 0.1 M Tris-HCl pH 8.5, 30 mM ala-pro, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.5365.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.047α = 90
b = 69.047β = 90
c = 124.622γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2007-05-14MSINGLE 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
12.175099.90.0660.04653.713.81665816658
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)
12.172.251000.5160.4186.213.71608

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2POE2.1724.78157971579184299.960.2270.227070.225740.2518RANDOM39.425
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]
0.020.02-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.12
r_dihedral_angle_3_deg12.997
r_dihedral_angle_1_deg5.637
r_dihedral_angle_4_deg2.744
r_scangle_it1.836
r_scbond_it1.211
r_angle_refined_deg1.077
r_mcangle_it1.022
r_mcbond_it0.572
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.12
r_dihedral_angle_3_deg12.997
r_dihedral_angle_1_deg5.637
r_dihedral_angle_4_deg2.744
r_scangle_it1.836
r_scbond_it1.211
r_angle_refined_deg1.077
r_mcangle_it1.022
r_mcbond_it0.572
r_nbtor_refined0.304
r_symmetry_hbond_refined0.254
r_nbd_refined0.184
r_symmetry_vdw_refined0.169
r_xyhbond_nbd_refined0.112
r_chiral_restr0.06
r_bond_refined_d0.008
r_gen_planes_refined0.003
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 Atoms1241
Nucleic Acid Atoms
Solvent Atoms120
Heterogen Atoms36

Software

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