1XEY

Crystal structure of the complex of Escherichia coli GADA with glutarate at 2.05 A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PMM	PDB ENTRY 1PMM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	290	PYRIDINE CHLORIDE, GLYCEROL,SODIUM CHLORIDE, SODIUM ACETATE, PEG 3000, pH 4.60, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.58	52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.1	α = 90
b = 117.1	β = 90
c = 196.4	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	IMAGE PLATE	MARRESEARCH		2002-04-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ELLIOTT GX-6	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.05	29.27	95.6	0.091	9.97		60197	60197	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.1	91.1		0.26	4.46

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1PMM	2.05	30	1	53367	53367	2857	89.34	0.151	0.151	0.14803	0.19861	RANDOM	23.201

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]
-0.89	-0.44		-0.89		1.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.94
r_scangle_it	4.33
r_scbond_it	2.64
r_mcangle_it	1.588
r_angle_refined_deg	1.446
r_mcbond_it	0.862
r_symmetry_vdw_refined	0.228
r_nbd_refined	0.202
r_symmetry_hbond_refined	0.157
r_xyhbond_nbd_refined	0.124

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.94
r_scangle_it	4.33
r_scbond_it	2.64
r_mcangle_it	1.588
r_angle_refined_deg	1.446
r_mcbond_it	0.862
r_symmetry_vdw_refined	0.228
r_nbd_refined	0.202
r_symmetry_hbond_refined	0.157
r_xyhbond_nbd_refined	0.124
r_chiral_restr	0.1
r_bond_refined_d	0.018
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7107
Nucleic Acid Atoms
Solvent Atoms	390
Heterogen Atoms	56

Software

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

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.