2HQQ

Crystal structure of human ketohexokinase complexed to different sugar molecules

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RKD	PDB ENTRY 1RKD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.7	291	0.7M ammonium sulphate, 0.5M lithium sulphate, 0.1M sodium citrate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.75	67.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.26	α = 90
b = 109.619	β = 90
c = 146.29	γ = 90

Symmetry
Space Group	I 2 2 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	ADSC QUANTUM 4	mirrors	2003-05-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX14.2	0.9795	SRS	PX14.2

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	1.86	87.706	99.8	0.063	0.063	6.6	7.3	41681	41681			27.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.86	1.96	99.2		0.325	0.325	5	7.3	6030

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	Single Isomorphous Replacement	THROUGHOUT	PDB ENTRY 1RKD	1.86	87.71	41795	37359	4129	99.27	0.20768	0.20474	0.23384	RANDOM	26.285

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]
-0.02			1.38		-1.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.599
r_dihedral_angle_4_deg	18.067
r_dihedral_angle_3_deg	13.294
r_dihedral_angle_1_deg	5.434
r_mcangle_it	2.03
r_scangle_it	2.026
r_mcbond_it	1.764
r_scbond_it	1.349
r_angle_refined_deg	1.296
r_angle_other_deg	0.702
r_mcbond_other	0.284
r_symmetry_vdw_other	0.27
r_nbd_refined	0.217
r_xyhbond_nbd_refined	0.212
r_nbd_other	0.203
r_symmetry_hbond_refined	0.2
r_nbtor_refined	0.188
r_symmetry_vdw_refined	0.132
r_nbtor_other	0.088
r_chiral_restr	0.075
r_xyhbond_nbd_other	0.065
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_metal_ion_refined
r_metal_ion_other
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	2277
Nucleic Acid Atoms
Solvent Atoms	268
Heterogen Atoms	15

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing