8JVF | pdb_00008jvf

Crystal structure of dephospho-coenzyme A kinase

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	PEG 1500, GTP

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.101	α = 90
b = 55.101	β = 90
c = 122.584	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	2.4	50	100	0.073	0.075	0.015	30.7	24.4		7963

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	2.4	2.49	100		0.417	0.425	0.082	10.7	26.5

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	2.4	41.01	7916	399	99.987	0.22	0.2185	0.22	0.2578	0.27	1	59.86

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]
2.62			2.62		-5.239

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.877
r_dihedral_angle_3_deg	15.721
r_lrange_it	12.903
r_lrange_other	12.903
r_scangle_it	10.158
r_scangle_other	10.152
r_mcangle_it	7.919
r_dihedral_angle_1_deg	7.918
r_mcangle_other	7.915
r_scbond_it	6.773
r_scbond_other	6.769
r_dihedral_angle_2_deg	6.528
r_mcbond_it	5.416
r_mcbond_other	5.411
r_angle_refined_deg	0.722
r_dihedral_angle_other_2_deg	0.585
r_nbd_other	0.27
r_angle_other_deg	0.24
r_symmetry_nbd_other	0.237
r_nbd_refined	0.223
r_nbtor_refined	0.171
r_symmetry_xyhbond_nbd_refined	0.168
r_xyhbond_nbd_refined	0.149
r_symmetry_nbd_refined	0.129
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.035
r_gen_planes_refined	0.01
r_bond_refined_d	0.002
r_gen_planes_other	0.001
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	993
Nucleic Acid Atoms
Solvent Atoms	19
Heterogen Atoms	33

Software

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