8OQW | pdb_00008oqw

Crystal structure of Tannerella forsythia MurNAc kinase MurK

X-RAY DIFFRACTION

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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		293	0.2-0.3 M ammonium sulfate, 14-22% (w/v) PEG3350, bis-tris/citric acid pH 4.1-6.4

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.759	α = 74.3
b = 59.51	β = 75.274
c = 96.708	γ = 65.953

Symmetry
Space Group	P 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 EIGER2 XE 16M		2018-07-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976	Diamond	I03

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	2.05	49.503	96.1	0.997	9.06	2.37		68635

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	2.05	2.17			0.751

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1X7F	2.05	49.503	68630	1716	96.216	0.202	0.2006	0.2	0.2486	0.25	37.311

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]
-0.936	0.221	-1.089	2.483	1.892	-1.828

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.358
r_dihedral_angle_6_deg	13.693
r_dihedral_angle_2_deg	11.515
r_dihedral_angle_1_deg	6.613
r_lrange_it	6.131
r_scangle_it	2.542
r_scbond_it	1.764
r_mcangle_it	1.619
r_angle_refined_deg	1.126
r_mcbond_it	1.027
r_nbtor_refined	0.307
r_nbd_refined	0.221
r_symmetry_nbd_refined	0.213
r_xyhbond_nbd_refined	0.147
r_symmetry_xyhbond_nbd_refined	0.146
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	8679
Nucleic Acid Atoms
Solvent Atoms	358
Heterogen Atoms	36

Software

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