8FV9 | pdb_00008fv9

E coli. CTP synthase in complex with F-dCTP

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

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 164.419	α = 90
b = 103.506	β = 90
c = 131.562	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	CCD	RAYONIX MX-300		2019-05-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08B1-1	0.978	CLSI	08B1-1

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.99	43.8	99.6	0.124	0.129	0.033	0.96	16.8	14.4		152954			33.6

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)	Redundancy	Number Unique Reflections (All)
1	1.99	2.06	96.1		0.878	0.95	0.346	0.648	1.98	6.9

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5TKV	1.991	43.8	152954	7768	99.573	0.191	0.1904	0.2	0.2049	0.21	36.084

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			-0.008		0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.625
r_dihedral_angle_3_deg	11.867
r_dihedral_angle_4_deg	11.753
r_dihedral_angle_1_deg	5.55
r_lrange_it	4.191
r_lrange_other	3.938
r_mcangle_it	1.864
r_mcangle_other	1.864
r_scangle_it	1.751
r_scangle_other	1.75
r_angle_refined_deg	1.165
r_angle_other_deg	1.098
r_mcbond_it	1.059
r_mcbond_other	1.059
r_scbond_it	1.003
r_scbond_other	1.003
r_nbd_refined	0.166
r_symmetry_nbd_other	0.155
r_nbd_other	0.143
r_nbtor_refined	0.142
r_symmetry_nbd_refined	0.129
r_xyhbond_nbd_refined	0.111
r_symmetry_xyhbond_nbd_refined	0.1
r_symmetry_nbtor_other	0.068
r_chiral_restr	0.046
r_symmetry_xyhbond_nbd_other	0.006
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	8312
Nucleic Acid Atoms
Solvent Atoms	822
Heterogen Atoms	86

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing