1ZYB

Crystal structure of transcription regulator from Bacteroides thetaiotaomicron VPI-5482 at 2.15 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1			273	4.0M NaFormate, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
3.86	67.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.98	α = 90
b = 115.98	β = 90
c = 119.639	γ = 120

Symmetry
Space Group	P 65 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 4	Double-crystal monochromator (Si 111), toroid	2005-05-05	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL1-5	0.979094, 0.918381	SSRL	BL1-5

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	2.1	29.91	99.9	0.088	0.088	6.4	6.8		28282

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	2.1	2.15		98.8	0.766	0.766	1	4.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.15	29.2	25047	1332	99.87	0.18	0.177	0.228	RANDOM	38.566

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]
-1.33	-0.66		-1.33		1.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.444
r_dihedral_angle_4_deg	15.613
r_dihedral_angle_3_deg	12.987
r_scangle_it	7.474
r_scbond_it	5.604
r_dihedral_angle_1_deg	5.56
r_mcangle_it	3.226
r_mcbond_it	2.395
r_angle_refined_deg	1.406
r_angle_other_deg	0.781
r_mcbond_other	0.529
r_symmetry_vdw_other	0.24
r_symmetry_hbond_refined	0.232
r_nbd_refined	0.21
r_nbtor_refined	0.181
r_symmetry_vdw_refined	0.179
r_nbd_other	0.173
r_xyhbond_nbd_refined	0.143
r_nbtor_other	0.085
r_chiral_restr	0.084
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1863
Nucleic Acid Atoms
Solvent Atoms	187
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
SOLVE	phasing