1RXQ | pdb_00001rxq

YfiT from Bacillus subtilis is a probable metal-dependent hydrolase with an unusual four-helix bundle topology

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	0.1M sodium cacodylate, 23% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.37	α = 104.38
b = 50.42	β = 90.61
c = 89.41	γ = 112.05

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		2003-12-04	M	SAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 5ID-B	0.979	APS	5ID-B

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	1.7	30		0.085	0.072	6.4	6.2	75437	70594		-3

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	1.7	1.744	67.1		0.298	0.21	3.1	3.8

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	1.7	30	74337	70594	3743	93.58	0.18798	0.18644	0.198	0.21708	0.2247	RANDOM	17.271

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]
0.18	0.27	0.09	0.18	0.12	-0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	6.909
r_scbond_it	4.989
r_dihedral_angle_1_deg	4.589
r_mcangle_it	3.334
r_mcbond_it	2.225
r_angle_refined_deg	0.898
r_angle_other_deg	0.667
r_symmetry_vdw_other	0.256
r_nbd_other	0.239
r_nbd_refined	0.211
r_metal_ion_refined	0.184
r_symmetry_vdw_refined	0.183
r_symmetry_hbond_refined	0.18
r_xyhbond_nbd_refined	0.177
r_nbtor_other	0.09
r_chiral_restr	0.059
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_gen_planes_other	0.004
r_bond_other_d	0.001
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_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	5690
Nucleic Acid Atoms
Solvent Atoms	469
Heterogen Atoms	41

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
SOLVE	phasing
RESOLVE	phasing