2GX5 | pdb_00002gx5

N-terminal GAF domain of transcriptional pleiotropic repressor CodY

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2B18	PDB ENTRY 2B18

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	291	ammonium sulphate, sodium citrate, PEG 400, 20mM cGMP, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.207	α = 90
b = 90.207	β = 90
c = 205.634	γ = 90

Symmetry
Space Group	P 43 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	CCD	ADSC QUANTUM 315		2005-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.97570	ESRF	ID23-1

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	1.74	50	98	0.083	22.11	7.2	85808	85808			26.6

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	1.74	1.8	95.2		0.612	1.67	3.7	8202

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 2B18	1.74	31.89	79437	79437	4191	97.46	0.18872	0.18872	0.18726	0.19	0.21595	0.19	RANDOM	23.72

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]
-0.21			-0.21		0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.992
r_dihedral_angle_4_deg	16.115
r_dihedral_angle_3_deg	15.72
r_dihedral_angle_1_deg	5.412
r_scangle_it	5.221
r_scbond_it	3.879
r_mcangle_it	3.416
r_rigid_bond_restr	3.407
r_sphericity_free	3.097
r_mcbond_it	2.622
r_sphericity_bonded	2.21
r_mcbond_other	1.092
r_angle_refined_deg	1.076
r_angle_other_deg	0.855
r_symmetry_vdw_other	0.222
r_symmetry_vdw_refined	0.218
r_nbd_refined	0.208
r_nbd_other	0.184
r_nbtor_refined	0.166
r_xyhbond_nbd_refined	0.134
r_symmetry_hbond_refined	0.122
r_nbtor_other	0.086
r_chiral_restr	0.07
r_xyhbond_nbd_other	0.026
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5039
Nucleic Acid Atoms
Solvent Atoms	388
Heterogen Atoms	171

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data scaling
MOLREP	phasing