8JVC

Crystal structure of dephospho-coenzyme A kinase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	PEG 3350, Bis-Tris (pH 6.5)

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.246	α = 90
b = 58.246	β = 90
c = 105.137	γ = 90

Symmetry
Space Group	P 43 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	PIXEL	DECTRIS PILATUS 6M		2020-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1.0000	SPring-8	BL45XU

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	2.15	41.22	100	0.107	0.11	0.022	24.9	25.1		10444

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	2.15	2.22			0.372	0.38	0.075	11.3

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	SAD	FREE R-VALUE	2.15	41.22	10393	487	99.952	0.199	0.197	0.2333	1	36.619

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]
-0.267			-0.267		0.535

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	18.401
r_dihedral_angle_3_deg	16.253
r_dihedral_angle_1_deg	8.109
r_lrange_it	7.658
r_lrange_other	7.658
r_scangle_it	5.79
r_scangle_other	5.787
r_dihedral_angle_2_deg	5.709
r_mcangle_it	4.602
r_mcangle_other	4.6
r_scbond_it	3.711
r_scbond_other	3.708
r_mcbond_it	3.146
r_mcbond_other	3.144
r_angle_refined_deg	0.621
r_symmetry_xyhbond_nbd_refined	0.258
r_symmetry_nbd_other	0.228
r_nbd_other	0.22
r_nbd_refined	0.217
r_angle_other_deg	0.203
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.151
r_symmetry_nbd_refined	0.122
r_symmetry_nbtor_other	0.08
r_symmetry_xyhbond_nbd_other	0.071
r_chiral_restr	0.032
r_gen_planes_refined	0.005
r_bond_refined_d	0.003
r_gen_planes_other	0.001
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1326
Nucleic Acid Atoms
Solvent Atoms	49
Heterogen Atoms

Software

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