8JVG

Crystal structure of dephospho-coenzyme A kinase

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8JVF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	PEG 3350, coenzyme A, sodium malonate

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.143	α = 90
b = 89.143	β = 90
c = 83.886	γ = 120

Symmetry
Space Group	P 61

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 EIGER X 4M		2020-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-1A	1.0000	Photon Factory	BL-1A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.5	44.611	100	0.052	0.053	0.011	42.1	20.9		13215

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.6			0.383	0.392	0.085	8.8

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.5	44.611	13184	682	99.962	0.209	0.2059	0.2735	1	51.621

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]
-0.181	-0.09		-0.181		0.587

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.248
r_dihedral_angle_3_deg	15.746
r_lrange_it	9.675
r_lrange_other	9.674
r_dihedral_angle_1_deg	8.038
r_scangle_it	7.44
r_scangle_other	7.438
r_dihedral_angle_2_deg	6.618
r_mcangle_it	5.872
r_mcangle_other	5.871
r_scbond_it	4.758
r_scbond_other	4.756
r_mcbond_it	3.975
r_mcbond_other	3.973
r_angle_refined_deg	0.474
r_nbd_other	0.27
r_symmetry_nbd_other	0.237
r_nbd_refined	0.224
r_symmetry_xyhbond_nbd_refined	0.21
r_nbtor_refined	0.174
r_angle_other_deg	0.163
r_symmetry_nbd_refined	0.16
r_xyhbond_nbd_refined	0.144
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.024
r_gen_planes_refined	0.01
r_gen_planes_other	0.003
r_bond_refined_d	0.001
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2504
Nucleic Acid Atoms
Solvent Atoms	37
Heterogen Atoms

Software

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