3A0I

Human glucokinase in complex with a synthetic activator

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1V4S	PDB ENTRY 1V4S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.6	298	30 % PEG 1500, HEPES, PH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.732	α = 90
b = 79.732	β = 90
c = 321.975	γ = 120

Symmetry
Space Group	P 65 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	DIFFRACTOMETER	WEISSENBERG		2002-04-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-6B	1.000	Photon Factory	BL-6B

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	2.2	50	94.5	0.064	0.064	16.5	5	32108	30342			36.1

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)
	2.2	2.28			0.254	1.86

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 1V4S	2.2	42.37	28759	1529	94.66	0.2285	0.22588	0.27702	RANDOM	35.812

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]
1.68	0.84		1.68		-2.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.394
r_dihedral_angle_4_deg	20.262
r_dihedral_angle_3_deg	19.34
r_dihedral_angle_1_deg	6.865
r_scangle_it	5.673
r_scbond_it	3.511
r_mcangle_it	2.358
r_angle_refined_deg	2.06
r_mcbond_it	1.305
r_symmetry_vdw_refined	0.449
r_symmetry_hbond_refined	0.369
r_nbtor_refined	0.31
r_nbd_refined	0.239
r_xyhbond_nbd_refined	0.191
r_chiral_restr	0.146
r_metal_ion_refined	0.142
r_bond_refined_d	0.024
r_gen_planes_refined	0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3505
Nucleic Acid Atoms
Solvent Atoms	137
Heterogen Atoms	43

Software

Software
Software Name	Purpose
REFMAC	refinement
WEIS	data scaling
HKL-2000	data reduction
HKL-2000	data scaling