8FV9

E coli. CTP synthase in complex with F-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
4.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 164.419α = 90
b = 103.506β = 90
c = 131.562γ = 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 08B1-10.978CLSI08B1-1

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
11.9943.899.60.1240.1290.0330.9616.814.415295433.6
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)
11.992.0696.10.8780.950.3460.6481.986.9

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-VALUE5TKV1.99143.8152954776899.5730.1910.19040.204936.084
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]
0.006-0.0080.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.625
r_dihedral_angle_3_deg11.867
r_dihedral_angle_4_deg11.753
r_dihedral_angle_1_deg5.55
r_lrange_it4.191
r_lrange_other3.938
r_mcangle_it1.864
r_mcangle_other1.864
r_scangle_it1.751
r_scangle_other1.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.625
r_dihedral_angle_3_deg11.867
r_dihedral_angle_4_deg11.753
r_dihedral_angle_1_deg5.55
r_lrange_it4.191
r_lrange_other3.938
r_mcangle_it1.864
r_mcangle_other1.864
r_scangle_it1.751
r_scangle_other1.75
r_angle_refined_deg1.165
r_angle_other_deg1.098
r_mcbond_it1.059
r_mcbond_other1.059
r_scbond_it1.003
r_scbond_other1.003
r_nbd_refined0.166
r_symmetry_nbd_other0.155
r_nbd_other0.143
r_nbtor_refined0.142
r_symmetry_nbd_refined0.129
r_xyhbond_nbd_refined0.111
r_symmetry_xyhbond_nbd_refined0.1
r_symmetry_nbtor_other0.068
r_chiral_restr0.046
r_symmetry_xyhbond_nbd_other0.006
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 Atoms8312
Nucleic Acid Atoms
Solvent Atoms822
Heterogen Atoms86

Software

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