8FV7

E coli. CTP synthase in complex with dF-dCTP + ATP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5TKV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82770.1 M TRIS-Cl pH 8.0 (room temperature), 5 mM magnesium chloride, 1.15 - 1.4 M ammonium sulfate, 15 mg/mL CTPS.
Crystal Properties
Matthews coefficientSolvent content
4.5472.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 158.982α = 90
b = 108.456β = 90
c = 128.9γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002021-12-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08B1-11.6532CLSI08B1-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim 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
12.0883.1261000.1350.1410.040.99412.412.513384635.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.082.151001.8621.9440.5560.6840.812

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5TKV2.0883.126133740661599.810.2040.2030.221539.846
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]
-1.4062.187-0.781
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.235
r_dihedral_angle_4_deg13.454
r_dihedral_angle_3_deg12.6
r_dihedral_angle_1_deg5.727
r_lrange_it4.713
r_lrange_other4.498
r_scangle_it2.347
r_scangle_other2.347
r_mcangle_it2.344
r_mcangle_other2.344
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.235
r_dihedral_angle_4_deg13.454
r_dihedral_angle_3_deg12.6
r_dihedral_angle_1_deg5.727
r_lrange_it4.713
r_lrange_other4.498
r_scangle_it2.347
r_scangle_other2.347
r_mcangle_it2.344
r_mcangle_other2.344
r_scbond_it1.351
r_scbond_other1.351
r_mcbond_it1.342
r_mcbond_other1.342
r_angle_refined_deg1.178
r_angle_other_deg1.097
r_nbd_refined0.17
r_symmetry_nbd_other0.159
r_nbd_other0.156
r_nbtor_refined0.143
r_xyhbond_nbd_refined0.123
r_metal_ion_refined0.111
r_symmetry_xyhbond_nbd_refined0.1
r_symmetry_nbd_refined0.097
r_symmetry_nbtor_other0.068
r_chiral_restr0.045
r_gen_planes_refined0.003
r_bond_refined_d0.002
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8334
Nucleic Acid Atoms
Solvent Atoms659
Heterogen Atoms126

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing