3JYR | pdb_00003jyr

Crystal structures of the GacH receptor of Streptomyces glaucescens GLA.O in the unliganded form and in complex with acarbose and an acarbose homolog. Comparison with acarbose-loaded maltose binding protein of Salmonella typhimurium.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	291	18% PEG 8000, 10 mM CITRATE, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.921	α = 90
b = 89.229	β = 112.77
c = 64.163	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 210	mirrors	2008-10-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.91841	BESSY	14.2

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	1.75	59.13	93.4	0.043	22.6	3.6		37653

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)
	1.75	1.81	64.6		0.12		2.3	2575

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.75	40	37652	1889	93.14	0.169	0.167	0.17	0.203	0.2	RANDOM	14.635

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]
0.58		0.55	-0.9		0.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.14
r_dihedral_angle_3_deg	13.805
r_dihedral_angle_4_deg	13.361
r_dihedral_angle_1_deg	5.312
r_scangle_it	3.235
r_scbond_it	2.011
r_angle_refined_deg	1.281
r_mcangle_it	1.129
r_mcbond_it	0.751
r_symmetry_vdw_refined	0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.14
r_dihedral_angle_3_deg	13.805
r_dihedral_angle_4_deg	13.361
r_dihedral_angle_1_deg	5.312
r_scangle_it	3.235
r_scbond_it	2.011
r_angle_refined_deg	1.281
r_mcangle_it	1.129
r_mcbond_it	0.751
r_symmetry_vdw_refined	0.36
r_nbtor_refined	0.307
r_nbd_refined	0.194
r_symmetry_hbond_refined	0.158
r_xyhbond_nbd_refined	0.116
r_chiral_restr	0.086
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2882
Nucleic Acid Atoms
Solvent Atoms	426
Heterogen Atoms	44

Software

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

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.