3HM8 | pdb_00003hm8

Crystal structure of the C-terminal Hexokinase domain of human HK3

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NZT	pdb entry 2NZT, chain A, residues 468 through 913

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.2	291	reservoir solution: 16% PEG 3350, 0.20 M Ammonium Citrate, 0.1 M HEPES. 0.005 M glucose-6-phosphate, 0.005 M ADP-Mg, 0.02 M TCEP, 1:100 (w/w) trypsin was added to the protein stock solution., pH 7.2, vapor diffusion, sitting drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3	58.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.904	α = 90
b = 83.904	β = 90
c = 323.327	γ = 90

Symmetry
Space Group	P 41

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	ADSC QUANTUM 315		2009-03-20		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID		APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.8	20	98.4				53686

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	2.8	2.9	86.8		0.666

Refinement

Statistics
Diffraction ID	Structure Solution 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)	Mean Isotropic B
X-RAY DIFFRACTION	MR	pdb entry 2NZT, chain A, residues 468 through 913	2.8	20	52939	1502	97.2	0.245	0.245	0.25	0.27	0.27	69.23

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]
5.541			5.541		-11.082

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.612
r_dihedral_angle_4_deg	12.304
r_dihedral_angle_3_deg	11.488
r_dihedral_angle_1_deg	3.864
r_angle_refined_deg	1.054
r_angle_other_deg	0.783
r_scangle_it	0.576
r_scbond_it	0.342
r_mcangle_it	0.137
r_mcbond_it	0.07
r_chiral_restr	0.059
r_mcbond_other	0.03
r_bond_refined_d	0.011
r_bond_other_d	0.003
r_gen_planes_refined	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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12521
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	112

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction