1IXC | pdb_00001ixc

Crystal structure of CbnR, a LysR family transcriptional regulator

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	Tris/HCl, MgSO4, NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.22	α = 90
b = 100.856	β = 90
c = 87.735	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	111	CCD	ADSC QUANTUM 4		2001-10-01	M	MAD
2	1	x-ray	105	CCD	ADSC QUANTUM 4		2002-01-30	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL40B2	0.9796, 0.9798, 0.9721, 0.9862	SPring-8	BL40B2
2	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-6A	0.978	Photon Factory	BL-6A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.2	35.6	100	0.053	0.053	9.4	7.2	32808	32808

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	2.2	2.32	100		0.235	0.265	0.265	7.3	4689

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 (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	MAD	THROUGHOUT	2.2	87.71	31092	31080	1676	99.9	0.21907	0.21907	0.21763	0.22	0.24527	0.25	RANDOM	16.122

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]
-0.91			-2.05		2.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	20.427
r_dihedral_angle_1_deg	4.872
r_scangle_it	2.593
r_scbond_it	1.521
r_angle_refined_deg	1.334
r_mcangle_it	1.087
r_angle_other_deg	0.725
r_mcbond_it	0.58
r_symmetry_hbond_refined	0.455
r_nbd_refined	0.354
r_nbd_other	0.2
r_symmetry_vdw_other	0.196
r_xyhbond_nbd_refined	0.173
r_symmetry_vdw_refined	0.109
r_chiral_restr	0.078
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_xyhbond_nbd_other	0.002
r_bond_other_d	0.001
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4436
Nucleic Acid Atoms
Solvent Atoms	128
Heterogen Atoms

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHARP	phasing
REFMAC	refinement
CCP4	data scaling