5KGH

X-ray structure of a glucosamine N-Acetyltransferase from Clostridium acetobutylicum, mutant Y297F

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5KF1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	293	8-11% PEG-8000, 100 mM homopipes,

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.294	α = 90
b = 65.941	β = 106.57
c = 90.449	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	CCD	Bruker Platinum 135		2016-01-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.8	50	98.1	0.08	0.08	11.3	6.6		66070

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	1.8	1.9	94.6		0.379	2.2	3

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5KF1	1.8	50	62715	3346	98.06	0.20693	0.20466	0.24887	RANDOM	26.281

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]
-0.05		0.46	-0.6		0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.98
r_dihedral_angle_4_deg	17.39
r_dihedral_angle_3_deg	15.767
r_dihedral_angle_1_deg	7.501
r_long_range_B_refined	6.371
r_long_range_B_other	6.37
r_scangle_other	4.709
r_mcangle_it	3.268
r_mcangle_other	3.268
r_scbond_it	3.107
r_scbond_other	3.105
r_mcbond_it	2.334
r_mcbond_other	2.333
r_angle_refined_deg	1.775
r_angle_other_deg	0.87
r_chiral_restr	0.104
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5195
Nucleic Acid Atoms
Solvent Atoms	419
Heterogen Atoms	165

Software

Software
Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
SADABS	data scaling
PHASER	phasing