3ID8

Ternary complex of human pancreatic glucokinase crystallized with activator, glucose and AMP-PNP

X-RAY DIFFRACTION

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	7.5	293	PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67	α = 90
b = 82.6	β = 90
c = 86.8	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	PIXEL	PSI PILATUS 6M		2008-11-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0	SLS	X06SA

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	2.4	19.94	95.8	0.09	0.08	16.8	6.3	19433	18612	2	2

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	2.4	2.5	91.5		0.42	0.39	5.2	6.5	2015

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1V4S	2.4	19.94	18338	966	100	0.20512	0.20123	0.27908	RANDOM	33.177

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]
0.92			1.03		-1.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.087
r_dihedral_angle_4_deg	19.341
r_dihedral_angle_3_deg	18.651
r_dihedral_angle_1_deg	5.864
r_scangle_it	2.698
r_scbond_it	1.625
r_angle_refined_deg	1.513
r_mcangle_it	1.158
r_mcbond_it	0.612
r_symmetry_hbond_refined	0.399

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.087
r_dihedral_angle_4_deg	19.341
r_dihedral_angle_3_deg	18.651
r_dihedral_angle_1_deg	5.864
r_scangle_it	2.698
r_scbond_it	1.625
r_angle_refined_deg	1.513
r_mcangle_it	1.158
r_mcbond_it	0.612
r_symmetry_hbond_refined	0.399
r_nbtor_refined	0.3
r_symmetry_vdw_refined	0.244
r_nbd_refined	0.23
r_metal_ion_refined	0.203
r_xyhbond_nbd_refined	0.177
r_chiral_restr	0.094
r_bond_refined_d	0.013
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3535
Nucleic Acid Atoms
Solvent Atoms	125
Heterogen Atoms	68

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.