2NZT

Crystal structure of human hexokinase II

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	291	16% PEG3350, 0.2M sodium malonate, 0.1M BTP, 10% ethylene glycol, 0.001M DDT, pH 8.5, vapor diffusion, sitting drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3	58
3	58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.89	α = 90
b = 129.338	β = 90
c = 187.232	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS		2006-08-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E	1.5418

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	2.45	30	99.8	0.082	15.3	5.5		85698

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)
	2.45	2.54		100	0.671		4.9

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 (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	pdb entry 1cza	2.45	25	83669	2083	98.172	0.232	0.2301	0.287	thin shells	42.349

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]
1.448			-2.777		1.329

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.155
r_dihedral_angle_4_deg	19.714
r_dihedral_angle_3_deg	15.766
r_dihedral_angle_1_deg	6.447
r_scangle_it	2.336
r_scbond_it	1.493
r_angle_refined_deg	1.427
r_angle_other_deg	1.349
r_mcangle_it	1.18
r_scangle_other	1.12
r_mcbond_it	0.713
r_scbond_other	0.665
r_mcangle_other	0.587
r_symmetry_vdw_other	0.333
r_nbd_refined	0.215
r_nbd_other	0.204
r_symmetry_hbond_refined	0.195
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.165
r_symmetry_vdw_refined	0.147
r_nbtor_other	0.094
r_chiral_restr	0.08
r_mcbond_other	0.072
r_bond_refined_d	0.017
r_gen_planes_refined	0.004
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13309
Nucleic Acid Atoms
Solvent Atoms	97
Heterogen Atoms	140

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Coot	model building
PRODRG	refinement
MolProbity	model building