4XSV

Human CTP: Phosphoethanolamine Cytidylyltransferase in complex with CTP


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.629317% PEG3350, 0.2M magnesium formate, 0.1M HEPES, 0.01M CTP, 0.01M magnesium chloride
Crystal Properties
Matthews coefficientSolvent content
2.4349.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.39α = 90
b = 73.39β = 90
c = 140.03γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42008-06-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.933300ESRFID14-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.74099.70.1310.12916.49.21111911119
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.899.60.5264.69.5

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 REPLACEMENTTHROUGHOUT3ELB2.739.371051755399.730.194770.1910.26417RANDOM34.017
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]
2.042.04-4.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.647
r_dihedral_angle_4_deg16.443
r_dihedral_angle_3_deg15.936
r_dihedral_angle_1_deg5.991
r_long_range_B_other5.413
r_long_range_B_refined5.411
r_scangle_other3.611
r_mcangle_it3.118
r_mcangle_other3.117
r_scbond_it2.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.647
r_dihedral_angle_4_deg16.443
r_dihedral_angle_3_deg15.936
r_dihedral_angle_1_deg5.991
r_long_range_B_other5.413
r_long_range_B_refined5.411
r_scangle_other3.611
r_mcangle_it3.118
r_mcangle_other3.117
r_scbond_it2.14
r_scbond_other2.139
r_mcbond_it1.873
r_mcbond_other1.87
r_angle_refined_deg1.512
r_angle_other_deg0.785
r_chiral_restr0.075
r_bond_refined_d0.012
r_gen_planes_refined0.006
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 Atoms2445
Nucleic Acid Atoms
Solvent Atoms21
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing