6Q5A

Crystal structure of Cryptosporidium hominis CPSF3 in the apo form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6Q55 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.527317% (v/v) Poly Ethylene Glycol 4000, 10% (v/v) Isopropanol, 100 mM HEPES pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.652.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.36α = 90
b = 90.36β = 90
c = 238.66γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2017-04-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.97625ESRFID30B

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
11.5548980.070.070.9915.710.182588
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)
11.551.6696.80.80.90.842.69.3

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 REPLACEMENTTHROUGHOUT6Q551.5547.4978391419798.030.139690.13760.17931RANDOM26.46
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]
-0.95-0.47-0.953.08
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free65.533
r_dihedral_angle_2_deg31.48
r_sphericity_bonded27.6
r_dihedral_angle_4_deg19.159
r_dihedral_angle_3_deg13.806
r_long_range_B_refined8.94
r_rigid_bond_restr7.283
r_long_range_B_other6.728
r_dihedral_angle_1_deg6.558
r_scangle_other4.133
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free65.533
r_dihedral_angle_2_deg31.48
r_sphericity_bonded27.6
r_dihedral_angle_4_deg19.159
r_dihedral_angle_3_deg13.806
r_long_range_B_refined8.94
r_rigid_bond_restr7.283
r_long_range_B_other6.728
r_dihedral_angle_1_deg6.558
r_scangle_other4.133
r_scbond_other3.295
r_scbond_it3.294
r_mcangle_it3.24
r_mcangle_other3.239
r_mcbond_it2.622
r_mcbond_other2.619
r_angle_refined_deg1.293
r_angle_other_deg0.919
r_chiral_restr0.068
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3613
Nucleic Acid Atoms
Solvent Atoms471
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing