8FVA | pdb_00008fva

E coli. CTP synthase in complex with F-araCTP

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 = 158.287	α = 90
b = 108.067	β = 90
c = 128.483	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	2.4	48.81	99.8	0.132	0.136	0.036	0.98	6.39	14.6		86531			48.6

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	2.4	2.49	99.8		0.399	1.036	0.272	0.934	2.47	14.5

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-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5TKV	2.4	48.81	86531	4335	99.807	0.206	0.205	0.2294	52.467

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			-0.002		0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.552
r_dihedral_angle_3_deg	13.106
r_dihedral_angle_4_deg	12.764
r_lrange_it	6.29
r_lrange_other	6.273
r_dihedral_angle_1_deg	5.882
r_scangle_it	4.014
r_scangle_other	4.014
r_mcangle_it	3.637
r_mcangle_other	3.637
r_scbond_it	2.321
r_scbond_other	2.321
r_mcbond_it	2.176
r_mcbond_other	2.176
r_angle_refined_deg	1.203
r_angle_other_deg	1.104
r_nbd_other	0.177
r_nbd_refined	0.173
r_symmetry_nbd_other	0.165
r_xyhbond_nbd_refined	0.154
r_symmetry_nbd_refined	0.147
r_nbtor_refined	0.145
r_metal_ion_refined	0.144
r_symmetry_xyhbond_nbd_refined	0.13
r_symmetry_nbtor_other	0.069
r_chiral_restr	0.046
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
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	213
Heterogen Atoms	67

Software

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