2HGV | pdb_00002hgv

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	7	291	PEG 5000, calcium acetate, valine, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.69	α = 90
b = 84.846	β = 90
c = 54.929	γ = 90

Symmetry
Space Group	P 21 21 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	MARMOSAIC 225 mm CCD		2005-04-25	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.9800	ESRF	BM14

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	2.3	30	99	0.104	13.7	6.1	7646	7646

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)
	2.3	2.38	92.2		0.361		4.2	672

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	2.3	27.72	7231	7231	350	100	0.16804	0.16804	0.16427	0.18	0.24418	0.26	RANDOM	39.09

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]
-0.01			0.18		-0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.5
r_dihedral_angle_4_deg	16.204
r_dihedral_angle_3_deg	15.735
r_dihedral_angle_1_deg	5.821
r_scangle_it	5.367
r_sphericity_free	4.256
r_scbond_it	3.738
r_mcangle_it	3.701
r_mcbond_it	2.83
r_sphericity_bonded	1.901
r_rigid_bond_restr	1.677
r_angle_refined_deg	1.408
r_mcbond_other	0.858
r_angle_other_deg	0.819
r_symmetry_hbond_refined	0.251
r_symmetry_vdw_other	0.249
r_symmetry_vdw_refined	0.221
r_nbd_refined	0.209
r_nbd_other	0.196
r_xyhbond_nbd_refined	0.193
r_nbtor_refined	0.17
r_nbtor_other	0.087
r_chiral_restr	0.077
r_bond_refined_d	0.013
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
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	1236
Nucleic Acid Atoms
Solvent Atoms	131
Heterogen Atoms	8

Software

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