Experiment: 7D4U

ATP complex with double mutant cyclic trinucleotide synthase CdnD

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7D4S	PDB 7D4S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	5 mM ATP, 10 mM GTP, 10 mM MgCl2, 5% w/v 1-butyl-3-methylimidazolium chloride, pH 7.4, 20% w/v PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.864	α = 90
b = 118.221	β = 90
c = 102.381	γ = 90

Symmetry
Space Group	C 2 2 21

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 MX300HE		2020-07-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL15A1	1.0000	NSRRC	BL15A1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.7	30	99.7	0.113	0.046	0.961	17.1	6.9		11739			41.63

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.8	99.2		0.633	0.26	0.838	2.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB 7D4S	2.7	24.24	1.35	11641	571	98.8	0.1951	0.1923	0.1937	0.2498	0.2513	42.8

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	21.56
f_angle_d	0.6482
f_chiral_restr	0.0396
f_plane_restr	0.0042
f_bond_d	0.0019

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2773
Nucleic Acid Atoms
Solvent Atoms	206
Heterogen Atoms	62

Software

Software
Software Name	Purpose
Blu-Ice	data collection
HKL-2000	data processing
CNS	phasing
PHENIX	refinement