3FGU | pdb_00003fgu

Catalytic complex of Human Glucokinase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3F9M	PDB ENTRY 3F9M

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
2.22	44.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.88	α = 90
b = 82.12	β = 90
c = 86.83	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		2008-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0001	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	2.15	25	84.5	0.076	0.067	17.2	3.6	26291	22231	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	2.15	2.27	84.8		0.33	0.27	3.1	2	2741

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3F9M	2.15	20	2	2	22231	21054	1125	84.5	0.19977	0.19673	0.21	0.25529	0.27	RANDOM	19.864

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]
1.12			0.46		-1.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.578
r_dihedral_angle_4_deg	20.122
r_dihedral_angle_3_deg	17.363
r_dihedral_angle_1_deg	5.689
r_scangle_it	2.635
r_scbond_it	1.617
r_angle_refined_deg	1.267
r_mcangle_it	1.108
r_angle_other_deg	0.923
r_mcbond_it	0.583
r_symmetry_vdw_other	0.293
r_nbd_refined	0.202
r_nbd_other	0.201
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.163
r_symmetry_hbond_refined	0.15
r_xyhbond_nbd_other	0.148
r_metal_ion_refined	0.124
r_mcbond_other	0.103
r_symmetry_vdw_refined	0.101
r_nbtor_other	0.086
r_chiral_restr	0.073
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3512
Nucleic Acid Atoms
Solvent Atoms	192
Heterogen Atoms	45

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling