7P9Y | pdb_00007p9y

N-acetylglucosamine kinase from Plesiomonas shigelloides compexed with alpha-N-acetylglucosamine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4DB3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		291	90 mM halogens; 0.1 M Na-HEPES/MOPS pH 7.5; 12.5% each MPD, PEG 1K, PEG 3350 Condition B8 of Morpheus screen (Molecular Dimensions)

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.476	α = 90
b = 115.476	β = 90
c = 119.657	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	PIXEL	DECTRIS PILATUS 6M		2018-08-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	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	1.94	57.74	100	0.999	11	6.7		68568

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	1.94	1.99			0.282

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	4DB3	1.94	46.136	68526	3517	99.975	0.211	0.209	0.21	0.2497	0.25	55.854

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]
0.288	0.144		0.288		-0.935

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.908
r_dihedral_angle_4_deg	16.51
r_dihedral_angle_3_deg	16.205
r_lrange_it	15.956
r_scangle_it	14.513
r_scbond_it	12.064
r_mcangle_it	11.197
r_mcbond_it	9.215
r_dihedral_angle_1_deg	6.278
r_angle_refined_deg	1.654
r_nbtor_refined	0.313
r_symmetry_nbd_refined	0.244
r_nbd_refined	0.227
r_xyhbond_nbd_refined	0.126
r_symmetry_xyhbond_nbd_refined	0.114
r_chiral_restr	0.11
r_ncsr_local_group_1	0.085
r_bond_refined_d	0.009
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4630
Nucleic Acid Atoms
Solvent Atoms	273
Heterogen Atoms	143

Software

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