8FV6 | pdb_00008fv6

E coli. CTP synthase in complex with dF-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	72.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 158.402	α = 90
b = 108.955	β = 90
c = 129.019	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	1	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	2.25	48.9	100	0.134	0.139	0.036	0.952	12.9	14.1		106448			38.9

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)	Redundancy	Number Unique Reflections (All)
1	2.25	2.33	99.9		0.82	0.853	0.233	0.798	2.06	13.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.25	48.9	106448	5316	99.905	0.191	0.1896	0.19	0.2099	0.21	46.454

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			-0.004		0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.022
r_dihedral_angle_3_deg	13.065
r_dihedral_angle_4_deg	12.49
r_dihedral_angle_1_deg	5.719
r_lrange_it	4.589
r_lrange_other	4.51
r_mcangle_it	2.708
r_mcangle_other	2.708
r_scangle_it	2.373
r_scangle_other	2.373
r_mcbond_it	1.535
r_mcbond_other	1.534
r_scbond_it	1.32
r_scbond_other	1.32
r_angle_refined_deg	1.177
r_angle_other_deg	1.081
r_nbd_other	0.186
r_symmetry_xyhbond_nbd_refined	0.167
r_nbd_refined	0.166
r_symmetry_nbd_other	0.162
r_symmetry_nbd_refined	0.155
r_nbtor_refined	0.143
r_xyhbond_nbd_refined	0.132
r_metal_ion_refined	0.112
r_symmetry_nbtor_other	0.07
r_chiral_restr	0.043
r_symmetry_xyhbond_nbd_other	0.019
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	8334
Nucleic Acid Atoms
Solvent Atoms	498
Heterogen Atoms	76

Software

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