8OQX | pdb_00008oqx

Crystal structure of Tannerella forsythia MurNAc kinase MurK with a phosphate analogue

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	0.12 - 0.14 M ammonium sulfate, Citric acid + Bis/Tris propane pH=5.5, PEG 3350 (14%-18% (w/v))

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.7	α = 90
b = 55.65	β = 93.596
c = 86	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS PILATUS 2M-F		2018-08-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.0	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	2.12	50	100	0.996	10.37	6.84		33324

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.12	2.18			0.996

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.12	48.61	33324	1667	99.979	0.191	0.1886	0.19	0.2351	0.24	33.655

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]
0.18		-0.295	-0.978		0.828

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	15.269
r_dihedral_angle_3_deg	14.469
r_dihedral_angle_6_deg	13.958
r_lrange_it	9.355
r_dihedral_angle_1_deg	6.391
r_scangle_it	4.357
r_scbond_it	3.4
r_mcangle_it	1.978
r_mcbond_it	1.369
r_angle_refined_deg	1.176

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	15.269
r_dihedral_angle_3_deg	14.469
r_dihedral_angle_6_deg	13.958
r_lrange_it	9.355
r_dihedral_angle_1_deg	6.391
r_scangle_it	4.357
r_scbond_it	3.4
r_mcangle_it	1.978
r_mcbond_it	1.369
r_angle_refined_deg	1.176
r_symmetry_xyhbond_nbd_refined	0.334
r_nbtor_refined	0.307
r_nbd_refined	0.212
r_symmetry_nbd_refined	0.188
r_xyhbond_nbd_refined	0.143
r_chiral_restr	0.092
r_gen_planes_refined	0.005
r_bond_refined_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4333
Nucleic Acid Atoms
Solvent Atoms	211
Heterogen Atoms	127

Software

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

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.