8FVC

E coli. CTP synthase in complex with dF-dCTP (potassium malonate + 5 mM MgCl2)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5TKV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	0.1 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 coefficient	Solvent content
4.54	72.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 165.796	α = 90
b = 103.967	β = 90
c = 131.888	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER2 X 16M		2022-01-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE 7B2	1.3777	CHESS	7B2

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.28	81.7	99.9	0.141	0.147	0.041	0.994	9.7	12.4		103987			42.2

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)	Redundancy	Number Unique Reflections (All)
1	2.28	2.36	98.8		1.15	1.243	0.458	0.629	0.8	7.11

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5TKV	2.281	81.7	103987	5239	99.721	0.195	0.1934	0.2185	45.715

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]
-1.888			3.558		-1.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.284
r_dihedral_angle_3_deg	12.679
r_dihedral_angle_4_deg	12.384
r_dihedral_angle_1_deg	5.736
r_lrange_it	5.168
r_lrange_other	5.101
r_scangle_it	3.091
r_scangle_other	3.091
r_mcangle_it	2.905
r_mcangle_other	2.904
r_scbond_it	1.744
r_scbond_other	1.743
r_mcbond_it	1.687
r_mcbond_other	1.687
r_angle_refined_deg	1.189
r_angle_other_deg	1.09
r_nbd_refined	0.167
r_symmetry_nbd_other	0.159
r_nbtor_refined	0.141
r_symmetry_nbd_refined	0.14
r_nbd_other	0.132
r_xyhbond_nbd_refined	0.119
r_symmetry_xyhbond_nbd_refined	0.09
r_symmetry_nbtor_other	0.068
r_symmetry_xyhbond_nbd_other	0.055
r_chiral_restr	0.045
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8326
Nucleic Acid Atoms
Solvent Atoms	476
Heterogen Atoms	88

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
MOLREP	phasing