3BY6 | pdb_00003by6

Crystal structure of a transcriptional regulator from Oenococcus oeni

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	289	0.2M NaCl, 0.1M Tris-HCl, 30% PEG 3000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
4.01	69.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.434	α = 90
b = 103.893	β = 102.85
c = 131.393	γ = 90

Symmetry
Space Group	C 1 2 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 315	Mirrors	2007-12-03	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9794, 0.9796	APS	19-ID

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	2.2	64.02	97.83	0.073	17.48	5	52664	51521		2	40

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	2.2	2.257	87.17		0.309	4.26	4.8	4108

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	MAD	THROUGHOUT	2.2	41.78	51521	51521	2778	97.83	0.24076	0.23875	0.24	0.27786	0.28	RANDOM	39.602

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]
2.93		-2.82	0.61		-4.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.524
r_dihedral_angle_4_deg	18.06
r_dihedral_angle_3_deg	17.403
r_dihedral_angle_1_deg	6.008
r_scangle_it	3.367
r_scbond_it	2.113
r_angle_refined_deg	1.515
r_mcangle_it	1.442
r_angle_other_deg	0.987
r_mcbond_it	0.889
r_metal_ion_refined	0.547
r_symmetry_hbond_refined	0.234
r_nbd_refined	0.228
r_symmetry_vdw_other	0.218
r_nbd_other	0.181
r_symmetry_vdw_refined	0.179
r_nbtor_refined	0.17
r_xyhbond_nbd_refined	0.164
r_mcbond_other	0.16
r_nbtor_other	0.089
r_chiral_restr	0.087
r_bond_refined_d	0.016
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4630
Nucleic Acid Atoms
Solvent Atoms	144
Heterogen Atoms	3

Software

Software
Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing