4ZCP

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829320% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.4549.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.52α = 90
b = 69.3β = 90
c = 116.44γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2015-02-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.8726ESRFID23-2

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
11.9858.2299.30.05910.54.613840

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 REPLACEMENTFREE R-VALUE4ZCT1.9858.221384071099.30.209230.20730.24713RANDOM40.135
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.788
r_dihedral_angle_4_deg15.769
r_dihedral_angle_3_deg11.852
r_long_range_B_refined6.617
r_long_range_B_other6.615
r_dihedral_angle_1_deg5.069
r_scangle_other3.795
r_mcangle_it3.147
r_mcangle_other3.146
r_scbond_it2.371
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.788
r_dihedral_angle_4_deg15.769
r_dihedral_angle_3_deg11.852
r_long_range_B_refined6.617
r_long_range_B_other6.615
r_dihedral_angle_1_deg5.069
r_scangle_other3.795
r_mcangle_it3.147
r_mcangle_other3.146
r_scbond_it2.371
r_scbond_other2.369
r_mcbond_it1.967
r_mcbond_other1.967
r_angle_refined_deg1.104
r_angle_other_deg0.673
r_chiral_restr0.067
r_bond_refined_d0.008
r_gen_planes_refined0.004
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 Atoms1023
Nucleic Acid Atoms
Solvent Atoms43
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
PHASERphasing
SCALAdata scaling
Cootmodel building
XDSdata reduction