3IDH

Human pancreatic glucokinase in complex with glucose

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

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.51	α = 90
b = 81.97	β = 90
c = 86.95	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	2.14	25	99	0.08	0.09	16.9	4.1		26185	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	2.14	2.26	98.6		0.41	0.48	3	3	3739

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	2.14	15	24739	1321	98.77	0.19041	0.18886	0.2201	RANDOM	22.912

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]
1.14			-0.7		-0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.155
r_dihedral_angle_4_deg	20.581
r_dihedral_angle_3_deg	17.161
r_dihedral_angle_1_deg	5.84
r_angle_other_deg	4.258
r_scangle_it	2.488
r_scbond_it	1.646
r_angle_refined_deg	1.309
r_mcangle_it	1.107
r_mcbond_it	0.619
r_symmetry_vdw_other	0.363
r_nbd_other	0.251
r_symmetry_vdw_refined	0.233
r_nbd_refined	0.207
r_metal_ion_refined	0.202
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.161
r_symmetry_hbond_refined	0.145
r_nbtor_other	0.109
r_chiral_restr	0.083
r_bond_refined_d	0.012
r_gen_planes_other	0.005
r_gen_planes_refined	0.004
r_bond_other_d
r_xyhbond_nbd_other
r_metal_ion_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	3557
Nucleic Acid Atoms
Solvent Atoms	225
Heterogen Atoms	13

Software

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