8FVA

E coli. CTP synthase in complex with F-araCTP


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 = 158.287α = 90
b = 108.067β = 90
c = 128.483γ = 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
12.448.8199.80.1320.1360.0360.986.3914.68653148.6
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)
12.42.4999.80.3991.0360.2720.9342.4714.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5TKV2.448.8186531433599.8070.2060.2050.229452.467
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]
-0.009-0.0020.011
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.552
r_dihedral_angle_3_deg13.106
r_dihedral_angle_4_deg12.764
r_lrange_it6.29
r_lrange_other6.273
r_dihedral_angle_1_deg5.882
r_scangle_it4.014
r_scangle_other4.014
r_mcangle_it3.637
r_mcangle_other3.637
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.552
r_dihedral_angle_3_deg13.106
r_dihedral_angle_4_deg12.764
r_lrange_it6.29
r_lrange_other6.273
r_dihedral_angle_1_deg5.882
r_scangle_it4.014
r_scangle_other4.014
r_mcangle_it3.637
r_mcangle_other3.637
r_scbond_it2.321
r_scbond_other2.321
r_mcbond_it2.176
r_mcbond_other2.176
r_angle_refined_deg1.203
r_angle_other_deg1.104
r_nbd_other0.177
r_nbd_refined0.173
r_symmetry_nbd_other0.165
r_xyhbond_nbd_refined0.154
r_symmetry_nbd_refined0.147
r_nbtor_refined0.145
r_metal_ion_refined0.144
r_symmetry_xyhbond_nbd_refined0.13
r_symmetry_nbtor_other0.069
r_chiral_restr0.046
r_bond_refined_d0.003
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8326
Nucleic Acid Atoms
Solvent Atoms213
Heterogen Atoms67

Software

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