2HLZ | pdb_00002hlz

Crystal Structure of human ketohexokinase

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	291	17% PEG8000, 5mM Cobalt Chloride, 200mM ammonium sulfate, 100mM NaCitrate, pH 4.2, vapor diffusion, sitting drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.8	55.8
2.8	55.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.933	α = 105.06
b = 71.672	β = 107.33
c = 82.694	γ = 93.09

Symmetry
Space Group	P 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	ADSC QUANTUM 210		2006-06-18	M	SINGLE WAVELENGTH
2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	0.97625	APS	17-ID

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	1.85	30	95.2	0.077	10	3.8		113793

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)
	1.85	1.92		77	0.438		3.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAS	1.85	29.656	113173	4258	94.572	0.216	0.2143	0.2229	0.249	0.2564	thin shells	15.727

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]
0.733	1.125	-0.201	0.371	-0.035	-1.121

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.512
r_dihedral_angle_4_deg	16.703
r_dihedral_angle_3_deg	12.883
r_dihedral_angle_1_deg	6.069
r_scangle_it	3.604
r_mcangle_it	3.135
r_scbond_it	2.745
r_mcbond_it	2.578
r_angle_refined_deg	1.382
r_angle_other_deg	0.95
r_mcbond_other	0.788
r_symmetry_vdw_other	0.267
r_nbd_refined	0.203
r_nbd_other	0.198
r_symmetry_vdw_refined	0.185
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.137
r_symmetry_hbond_refined	0.1
r_nbtor_other	0.083
r_chiral_restr	0.082
r_bond_refined_d	0.016
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9045
Nucleic Acid Atoms
Solvent Atoms	372
Heterogen Atoms	32

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ARP/wARP	model building
MolProbity	model building