8FV6

E coli. CTP synthase in complex with dF-dCTP


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 = 158.402α = 90
b = 108.955β = 90
c = 129.019γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002019-05-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08B1-11CLSI08B1-1

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
12.2548.91000.1340.1390.0360.95212.914.110644838.9
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)
12.252.3399.90.820.8530.2330.7982.0613.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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-VALUE2.2548.9106448531699.9050.1910.18960.209946.454
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]
0.001-0.0040.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.022
r_dihedral_angle_3_deg13.065
r_dihedral_angle_4_deg12.49
r_dihedral_angle_1_deg5.719
r_lrange_it4.589
r_lrange_other4.51
r_mcangle_it2.708
r_mcangle_other2.708
r_scangle_it2.373
r_scangle_other2.373
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.022
r_dihedral_angle_3_deg13.065
r_dihedral_angle_4_deg12.49
r_dihedral_angle_1_deg5.719
r_lrange_it4.589
r_lrange_other4.51
r_mcangle_it2.708
r_mcangle_other2.708
r_scangle_it2.373
r_scangle_other2.373
r_mcbond_it1.535
r_mcbond_other1.534
r_scbond_it1.32
r_scbond_other1.32
r_angle_refined_deg1.177
r_angle_other_deg1.081
r_nbd_other0.186
r_symmetry_xyhbond_nbd_refined0.167
r_nbd_refined0.166
r_symmetry_nbd_other0.162
r_symmetry_nbd_refined0.155
r_nbtor_refined0.143
r_xyhbond_nbd_refined0.132
r_metal_ion_refined0.112
r_symmetry_nbtor_other0.07
r_chiral_restr0.043
r_symmetry_xyhbond_nbd_other0.019
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 Atoms498
Heterogen Atoms76

Software

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