2YVH | pdb_00002yvh

Crystal structure of the operator-binding form of the multi-drug binding transcriptional repressor CgmR

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	0.05M Tris-HCl, 0.1M CaCl2, 4% PEG 400, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.011	α = 108.98
b = 80.095	β = 102.25
c = 87.056	γ = 96.14

Symmetry
Space Group	P 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	mirror	2006-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	0.97909	Photon Factory	AR-NW12A

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	2.5	100	98.2	0.091	12.5	7.8	32512	32512	-3		46.7

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	2.5	2.59	98		0.48		7.3	3252

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	SAD	THROUGHOUT	2.5	10	31983	30388	1595	98.23	0.22213	0.22023	0.2352	0.25854	0.2333	RANDOM	53.419

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]
0.53	-0.32	-3.16	-1.41	-0.8	-1.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.883
r_dihedral_angle_3_deg	23.504
r_dihedral_angle_4_deg	17.337
r_dihedral_angle_1_deg	6.498
r_scangle_it	3.626
r_scbond_it	2.422
r_angle_refined_deg	2.165
r_mcangle_it	1.809
r_mcbond_it	1.097
r_nbtor_refined	0.316

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.883
r_dihedral_angle_3_deg	23.504
r_dihedral_angle_4_deg	17.337
r_dihedral_angle_1_deg	6.498
r_scangle_it	3.626
r_scbond_it	2.422
r_angle_refined_deg	2.165
r_mcangle_it	1.809
r_mcbond_it	1.097
r_nbtor_refined	0.316
r_symmetry_hbond_refined	0.29
r_nbd_refined	0.253
r_symmetry_vdw_refined	0.244
r_xyhbond_nbd_refined	0.203
r_chiral_restr	0.133
r_bond_refined_d	0.017
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5530
Nucleic Acid Atoms	1136
Solvent Atoms	3
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	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.