1WPB | pdb_00001wpb

Structure of Escherichia coli yfbU gene product

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	sodium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.8	55.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 230.521	α = 90
b = 230.521	β = 90
c = 230.521	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	CUSTOM-MADE			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID		APS	19-ID

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	50	100	0.076	0.076	28.6	10.9		272350		-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	2	2.03	99.9		0.951	0.951	1.91	8.8	11646

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	SIR	THROUGHOUT	2	15	-3	271727	270667	1366	99.96	0.21245	0.1897	0.18951	0.2113	0.22652	0.2473	RANDOM	34.183

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	34.507
r_dihedral_angle_4_deg	19.269
r_dihedral_angle_3_deg	15.147
r_dihedral_angle_1_deg	6.484
r_scangle_it	3.613
r_scbond_it	2.493
r_mcangle_it	1.646
r_angle_refined_deg	1.62
r_mcbond_it	1.489
r_angle_other_deg	0.984
r_mcbond_other	0.287
r_symmetry_vdw_other	0.262
r_nbd_refined	0.224
r_symmetry_hbond_refined	0.213
r_symmetry_vdw_refined	0.211
r_nbtor_refined	0.188
r_xyhbond_nbd_refined	0.186
r_nbd_other	0.18
r_xyhbond_nbd_other	0.125
r_chiral_restr	0.116
r_nbtor_other	0.087
r_symmetry_hbond_other	0.043
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	22375
Nucleic Acid Atoms
Solvent Atoms	1618
Heterogen Atoms	300

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELXD	phasing
REFMAC	refinement