2YHW | pdb_00002yhw

High-resolution crystal structures of N-Acetylmannosamine kinase: Insights about substrate specificity, activity and inhibitor modelling.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				0.2 M CALCIUM ACETATE, 0.1 M SODIUM CACODYLATE PH 6.5 AND 40% PEG 300.

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.73	α = 90
b = 90.73	β = 90
c = 100.78	γ = 90

Symmetry
Space Group	P 41 21 2

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	MARMOSAIC 225 mm CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2		BESSY	14.2

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	1.64	45.3	100	0.06	30.66	12.9		52083		4.37

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	OTHER	THROUGHOUT	NONE	1.64	45.37	49478	2605	100	0.14933	0.1482	0.16	0.17019	0.18	RANDOM	25.699

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]
0.39			0.39		-0.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.213
r_dihedral_angle_4_deg	19.749
r_dihedral_angle_3_deg	14.316
r_dihedral_angle_1_deg	6.637
r_scangle_it	5.643
r_scbond_it	3.468
r_mcangle_it	2.122
r_angle_refined_deg	2.068
r_mcbond_it	1.274
r_angle_other_deg	1.184
r_mcbond_other	0.435
r_chiral_restr	0.157
r_bond_refined_d	0.026
r_gen_planes_refined	0.01
r_gen_planes_other	0.004
r_bond_other_d	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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2271
Nucleic Acid Atoms
Solvent Atoms	255
Heterogen Atoms	71

Software

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