4DZ6 | pdb_00004dz6

Transition state mimic of nucleoside-diphosphate kinase from borrelia burgdorferi with bound vanadate and adp

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4DI6	pdb entry 4DI6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289	EBS INTERNAL TRACKING NUMBER ACTIVATED SODIUM ORTHOVANADATE, 2 MM ADP, BOBUA.00664.A.A1_ PS00257 AT 17 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.65	α = 90
b = 81	β = 90
c = 181.43	γ = 90

Symmetry
Space Group	P 21 21 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	MARCCD 300		2012-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	2.2	99.47	99.6	0.053	17.32			87269		-3	40.87

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	2.2	2.26	99.47		0.311	3.6

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	pdb entry 4DI6	2.2	99.47	59351	3003		0.185	0.183	0.18	0.223	0.22	RANDOM	36.587

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]
0.31			-1.51		1.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.38
r_dihedral_angle_3_deg	15.017
r_dihedral_angle_4_deg	13.85
r_dihedral_angle_1_deg	5.808
r_angle_refined_deg	1.406
r_chiral_restr	0.098
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8065
Nucleic Acid Atoms
Solvent Atoms	328
Heterogen Atoms	116

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement

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.