4ZCS

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HL4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.92930.2M NaF, 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
3.0159.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.631α = 90
b = 149.132β = 90
c = 175.598γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2014-01-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.979338ESRFID23-1

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
12.45113.6799.630.320.29.3552521

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 REPLACEMENTTHROUGHOUT3HL42.45113.6752521280899.630.183250.180590.23413RANDOM44.051
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]
0.07-0.090.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.454
r_dihedral_angle_4_deg21.093
r_dihedral_angle_3_deg15.972
r_long_range_B_refined9.192
r_long_range_B_other9.192
r_dihedral_angle_1_deg7.022
r_scangle_other6.697
r_mcangle_it6.127
r_mcangle_other6.127
r_scbond_it4.364
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.454
r_dihedral_angle_4_deg21.093
r_dihedral_angle_3_deg15.972
r_long_range_B_refined9.192
r_long_range_B_other9.192
r_dihedral_angle_1_deg7.022
r_scangle_other6.697
r_mcangle_it6.127
r_mcangle_other6.127
r_scbond_it4.364
r_scbond_other4.363
r_mcbond_it4.065
r_mcbond_other4.065
r_angle_refined_deg1.97
r_angle_other_deg1.134
r_chiral_restr0.11
r_bond_refined_d0.019
r_gen_planes_refined0.008
r_bond_other_d0.004
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6806
Nucleic Acid Atoms
Solvent Atoms341
Heterogen Atoms224

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building