4ZCR

Crystal structure of the C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase in complex with phosphocholine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4ZCT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829320% PEG 4k
Crystal Properties
Matthews coefficientSolvent content
2.4950.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.62α = 90
b = 69.57β = 90
c = 117.86γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-03-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.972957ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.846.5199.630.05414.36.418719

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 REPLACEMENTTHROUGHOUT4ZCT1.846.511871992799.630.178920.176410.2322RANDOM47.198
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]
-0.090.070.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.703
r_sphericity_free26.232
r_dihedral_angle_4_deg21.918
r_dihedral_angle_3_deg12.612
r_sphericity_bonded9.456
r_dihedral_angle_1_deg6.774
r_long_range_B_refined4.354
r_long_range_B_other4.352
r_scangle_other3.859
r_mcangle_it3.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.703
r_sphericity_free26.232
r_dihedral_angle_4_deg21.918
r_dihedral_angle_3_deg12.612
r_sphericity_bonded9.456
r_dihedral_angle_1_deg6.774
r_long_range_B_refined4.354
r_long_range_B_other4.352
r_scangle_other3.859
r_mcangle_it3.76
r_mcangle_other3.757
r_mcbond_other3.606
r_mcbond_it3.602
r_scbond_it3.178
r_scbond_other3.175
r_rigid_bond_restr1.992
r_angle_refined_deg1.218
r_angle_other_deg1.076
r_chiral_restr0.069
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.003
r_gen_planes_other0.002
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 Atoms1040
Nucleic Acid Atoms
Solvent Atoms91
Heterogen Atoms11

Software

Software
Software NamePurpose
REFMACrefinement
PHASERphasing
XDSdata scaling
Cootmodel building