6Q55

Crystal structure of Cryptosporidium hominis CPSF3 in complex with Compound 61


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2I7Vhomology model based on 2I7V

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.527717% (v/v) Poly Ethylene Glycol 4000, 10% (v/v) Isopropanol, 100 mM HEPES pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.652.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.67α = 90
b = 90.67β = 90
c = 237.59γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-02-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.97941ESRFID30B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)CC (Half)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
126099.60.120.130.9910.37.839853
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0599.60.240.250.2617.8

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUThomology model based on 2I7V247.4237874197999.630.183350.181310.22244RANDOM49.384
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]
0.440.220.44-1.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.763
r_dihedral_angle_4_deg22.989
r_dihedral_angle_3_deg16.2
r_long_range_B_refined10.826
r_long_range_B_other10.826
r_scangle_other7.692
r_dihedral_angle_1_deg6.992
r_mcangle_other5.976
r_mcangle_it5.967
r_scbond_it5.125
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.763
r_dihedral_angle_4_deg22.989
r_dihedral_angle_3_deg16.2
r_long_range_B_refined10.826
r_long_range_B_other10.826
r_scangle_other7.692
r_dihedral_angle_1_deg6.992
r_mcangle_other5.976
r_mcangle_it5.967
r_scbond_it5.125
r_scbond_other5.106
r_mcbond_it3.999
r_mcbond_other3.981
r_angle_refined_deg1.504
r_angle_other_deg0.883
r_chiral_restr0.125
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3613
Nucleic Acid Atoms
Solvent Atoms214
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing