4DCH

Insights into Glucokinase Activation Mechanism: Observation of Multiple Distinct Protein Conformations

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.4	286	20% PEG 3350, 0.1A citrate pH 5.4, 0.2M ammonium iodide, 50mM glucose, VAPOR DIFFUSION, HANGING DROP, temperature 286K

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.917	α = 90
b = 85.794	β = 104.4
c = 72.939	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	CCD	ADSC QUANTUM 315		2005-07-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	1.00	ALS	5.0.1

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	1.8	50	97.2	0.068	11.2	3.4	54275	54275	1	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)
1	1.8	1.86	75.5		0.408		2.2	4177

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.79	50	54252	54252	2747	97.12	0.1998	0.1998	0.1981	0.2313	RANDOM	29.7263

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]
0.06		-0.69	-0.2		-0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.434
r_dihedral_angle_4_deg	18.249
r_dihedral_angle_3_deg	14.243
r_dihedral_angle_1_deg	5.543
r_scangle_it	4.163
r_scbond_it	2.614
r_mcangle_it	1.693
r_angle_refined_deg	1.472
r_mcbond_it	1.055
r_nbtor_refined	0.296

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.434
r_dihedral_angle_4_deg	18.249
r_dihedral_angle_3_deg	14.243
r_dihedral_angle_1_deg	5.543
r_scangle_it	4.163
r_scbond_it	2.614
r_mcangle_it	1.693
r_angle_refined_deg	1.472
r_mcbond_it	1.055
r_nbtor_refined	0.296
r_symmetry_hbond_refined	0.207
r_nbd_refined	0.198
r_symmetry_vdw_refined	0.195
r_xyhbond_nbd_refined	0.156
r_chiral_restr	0.105
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3382
Nucleic Acid Atoms
Solvent Atoms	311
Heterogen Atoms	39

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Web-Ice	data collection
DENZO	data reduction

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.