4I1V | pdb_00004i1v

Crystal structure of a dephospho-CoA kinase from Burkholderia vietnamiensis bound to ADP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4I1U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	BuviA.00139.a.B1 PS01581 at 26.1 mg/mL with 2 mM ADP against Morpheus screen condition F1, 10% PEG 20,000, 20% PEG 550 MME, 0.02 M each monosaccharide, 0.1 M MES/imidazole pH 6.5, crystal tracking ID 237917f1, unique puck ID beh5-16, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
3.87	68.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.86	α = 90
b = 115.86	β = 90
c = 91.64	γ = 120

Symmetry
Space Group	P 32 2 1

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	ADSC QUANTUM 315r		2012-10-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.9774	ALS	5.0.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.6	50	99.7	0.046	26.18	5.2	22230	22169		-3	59.114

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.67	99.8		0.5	3.7

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4i1u	2.6	44.04	22169	1130	99.73	0.2148	0.2128	0.21	0.2518	0.25	RANDOM	63.8381

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]
0.69	0.69		0.69		-2.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.442
r_dihedral_angle_3_deg	15.117
r_dihedral_angle_4_deg	12.708
r_dihedral_angle_1_deg	5.813
r_angle_refined_deg	1.469
r_angle_other_deg	0.954
r_chiral_restr	0.074
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.442
r_dihedral_angle_3_deg	15.117
r_dihedral_angle_4_deg	12.708
r_dihedral_angle_1_deg	5.813
r_angle_refined_deg	1.469
r_angle_other_deg	0.954
r_chiral_restr	0.074
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.004
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2963
Nucleic Acid Atoms
Solvent Atoms	53
Heterogen Atoms	54

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.