4L3Q | pdb_00004l3q

Crystal structure of glucokinase-activator complex

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		293	VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.86	57.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.512	α = 90
b = 79.512	β = 90
c = 321.131	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	98	IMAGE PLATE	MAR scanner 345 mm plate	Mirrors	2004-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418

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	2.7	50	97.4	0.042	32.3		17490	17045	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	2.7	2.8	99.8		0.155	9.3	4.1	1678

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 1V4S	2.7	39.84	15665	1769	99.59	0.2591	0.25415	0.243	0.30377	0.2925	RANDOM	52.461

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]
-0.1	-0.05		-0.1		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.872
r_scangle_it	3.439
r_scbond_it	1.946
r_mcangle_it	1.683
r_angle_refined_deg	1.511
r_mcbond_it	0.89
r_symmetry_hbond_refined	0.281
r_nbd_refined	0.237
r_symmetry_vdw_refined	0.236
r_xyhbond_nbd_refined	0.143
r_chiral_restr	0.116
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3499
Nucleic Acid Atoms
Solvent Atoms	6
Heterogen Atoms	32

Software

Software
Software Name	Purpose
MAR345dtb	data collection
CNX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNX	phasing