3VGM | pdb_00003vgm

Crystal structure of a ROK family glucokinase from Streptomyces griseus in complex with glucose

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2AA4	PDB ENTRY 2AA4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.1	293	0.9M K/Na tartrate, 0.2M NaCl, 0.1M imidazole , pH 8.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.57	65.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.19	α = 90
b = 108.19	β = 90
c = 141.18	γ = 120

Symmetry
Space Group	P 64 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	95	CCD	ADSC QUANTUM 270		2008-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	1.00000	Photon Factory	BL-17A

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	1.84	20	99.8	0.041	32.89			42812		-3	31.781

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.84	1.89	98.9		0.33	0.365	4.31

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2AA4	1.84	20	42812	2159	99.76	0.1683	0.1674	0.17	0.185	0.19	RANDOM	26.4135

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]
0.86	0.43		0.86		-1.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.968
r_dihedral_angle_4_deg	14.953
r_dihedral_angle_3_deg	12.587
r_dihedral_angle_1_deg	5.169
r_scangle_it	4.439
r_scbond_it	2.678
r_mcangle_it	1.599
r_angle_refined_deg	1.286
r_mcbond_it	0.825
r_chiral_restr	0.097

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.968
r_dihedral_angle_4_deg	14.953
r_dihedral_angle_3_deg	12.587
r_dihedral_angle_1_deg	5.169
r_scangle_it	4.439
r_scbond_it	2.678
r_mcangle_it	1.599
r_angle_refined_deg	1.286
r_mcbond_it	0.825
r_chiral_restr	0.097
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2271
Nucleic Acid Atoms
Solvent Atoms	253
Heterogen Atoms	14

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

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.