4LR3 | pdb_00004lr3

Crystal structure of E. coli YfbU at 2.5 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	289	1.6 M ammonium phosphate monobasic, 100 mM MES, pH 5.5 or 100 mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
3.24	62.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 230.078	α = 90
b = 230.078	β = 90
c = 230.078	γ = 90

Symmetry
Space Group	P 2 3

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 315r		2013-03-28	M	SINGLE WAVELENGTH
2	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2013-02-22	M	SINGLE WAVELENGTH
3	1	x-ray	100	CCD	ADSC QUANTUM 315r		2013-03-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.2146	NSLS	X29A
2	SYNCHROTRON	APS BEAMLINE 24-ID-C	1.0086	APS	24-ID-C
3	SYNCHROTRON	NSLS BEAMLINE X29A	0.9790	NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.5	56	99.1			139809	138551

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2,3	2.5

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/SIR	THROUGHOUT	2.5	55.8	139809	131307	6945	99.14	0.20986	0.20789	0.21	0.24703	0.25	RANDOM	45.572

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.069
r_sphericity_free	22.921
r_dihedral_angle_4_deg	19.071
r_dihedral_angle_3_deg	16.296
r_sphericity_bonded	7.641
r_dihedral_angle_1_deg	4.818
r_scbond_it	3.167
r_mcangle_it	2.84
r_rigid_bond_restr	2.673
r_mcbond_it	2.375
r_mcbond_other	2.375
r_angle_refined_deg	1.298
r_angle_other_deg	1.125
r_chiral_restr	0.061
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	21904
Nucleic Acid Atoms
Solvent Atoms	1335
Heterogen Atoms	147

Software

Software
Software Name	Purpose
CBASS	data collection
SOLVE	phasing
MLPHARE	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling