1SBR | pdb_00001sbr

The structure and function of B. subtilis YkoF gene product: the complex with thiamin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1S99

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5	295	20% PEG 8000, 0.2 M calcium acetate, 0.1 M MES , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K, pH 6.50

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.82	α = 90
b = 82.49	β = 90
c = 86.11	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	120	IMAGE PLATE	RIGAKU RAXIS IV	MIRRORS	2003-09-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS

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	2.3	30		0.075	18.4	4.7		16658		-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)
	2.3	2.38	49.7		0.306	2.8	3.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	MOLECULAR REPLACEMENT	THROUGHOUT	1S99	2.3	20	15723	836	100	0.20915	0.20603	0.21	0.26881	0.26	RANDOM	55.8

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]
10.65			-4.17		-6.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.971
r_scangle_it	3.861
r_scbond_it	2.637
r_angle_refined_deg	1.669
r_mcangle_it	1.663
r_mcbond_it	0.883
r_nbd_refined	0.23
r_symmetry_vdw_refined	0.2
r_chiral_restr	0.186
r_xyhbond_nbd_refined	0.152
r_metal_ion_refined	0.141
r_bond_refined_d	0.019
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_refined
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	2788
Nucleic Acid Atoms
Solvent Atoms	77
Heterogen Atoms	73

Software

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