3GOI | pdb_00003goi

Human glucokinase in complex with a synthetic activator

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.6	298	30% PEG 1500, HEPES, pH6.6, vapor diffusion, hanging drop, temperature 298K, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.94	58.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.085	α = 90
b = 80.085	β = 90
c = 323.974	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	mirrors	2001-10-02	M	SINGLE WAVELENGTH

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

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	2.52	50	98.3	0.047	71.222	20.3		21669

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)
	2.52	2.61	91.1		0.143		18.8	1923

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	FOURIER SYNTHESIS	THROUGHOUT	2.52	47.35	21611	1103	99.07	0.209	0.205	0.1984	0.282	0.2691	RANDOM	30.707

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.905
r_dihedral_angle_3_deg	20.831
r_dihedral_angle_4_deg	19.584
r_dihedral_angle_1_deg	8.277
r_scangle_it	6.137
r_scbond_it	3.974
r_angle_refined_deg	2.563
r_mcangle_it	2.492
r_mcbond_it	1.503
r_symmetry_hbond_refined	0.336
r_nbtor_refined	0.335
r_nbd_refined	0.266
r_symmetry_vdw_refined	0.224
r_xyhbond_nbd_refined	0.205
r_chiral_restr	0.176
r_bond_refined_d	0.03
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3505
Nucleic Acid Atoms
Solvent Atoms	128
Heterogen Atoms	36

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction