1RKT

Crystal structure of yfiR, a putative transcriptional regulator from Bacillus subtilis

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.8	277	10mM CaCl2, 0.1M MES, 30% MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 5.8

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.983	α = 71.96
b = 48.765	β = 70.65
c = 57.233	γ = 80.2

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	77	CCD	MARRESEARCH		2003-08-14	M	SAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 5ID-B	0.9791	APS	5ID-B

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	1.95	30		0.045	16.318	4	35124	33929		-3

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	1.95	1.97	88.4		0.279	2.6	2

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.95	30	31133	31133	1653	96.99	0.21047	0.20808	0.25417	RANDOM	24.601

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]
1.11	1.85	-0.3	-1.94	0.34	0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	8.749
r_scbond_it	6.323
r_mcangle_it	4.442
r_dihedral_angle_1_deg	4.427
r_mcbond_it	3.378
r_angle_refined_deg	0.947
r_angle_other_deg	0.917
r_symmetry_vdw_other	0.354
r_symmetry_hbond_refined	0.301
r_nbd_other	0.244
r_symmetry_vdw_refined	0.241
r_nbd_refined	0.237
r_xyhbond_nbd_refined	0.215
r_nbtor_other	0.09
r_chiral_restr	0.055
r_bond_refined_d	0.01
r_bond_other_d	0.003
r_gen_planes_refined	0.003
r_gen_planes_other	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3296
Nucleic Acid Atoms
Solvent Atoms	123
Heterogen Atoms	39

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing