2QY6 | pdb_00002qy6

Crystal structure of the N-terminal domain of UPF0209 protein yfcK from Escherichia coli O157:H7

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	294	4M Sodium formate, pH 7.0, VAPOR DIFFUSION, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.067	α = 90
b = 80.468	β = 90
c = 234.376	γ = 90

Symmetry
Space Group	C 2 2 21

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	MAR CCD 165 mm		2007-08-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97958	APS	31-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	117.188	99.9	0.167	0.167	6.5	6.4	46490	46444			35.3

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	2.11	100		0.719	0.719	1.6	6.6	6647

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		THROUGHOUT	2	20	46386	46386	2343	99.98	0.227	0.225	0.23	0.268	0.28	RANDOM	49.968

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]
2.61			0.71		-3.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.726
r_dihedral_angle_4_deg	21.822
r_dihedral_angle_3_deg	16.279
r_dihedral_angle_1_deg	6.876
r_scangle_it	4.417
r_scbond_it	2.759
r_mcangle_it	1.712
r_angle_refined_deg	1.544
r_mcbond_it	1.114
r_nbtor_refined	0.312

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.726
r_dihedral_angle_4_deg	21.822
r_dihedral_angle_3_deg	16.279
r_dihedral_angle_1_deg	6.876
r_scangle_it	4.417
r_scbond_it	2.759
r_mcangle_it	1.712
r_angle_refined_deg	1.544
r_mcbond_it	1.114
r_nbtor_refined	0.312
r_nbd_refined	0.206
r_symmetry_vdw_refined	0.193
r_symmetry_hbond_refined	0.18
r_xyhbond_nbd_refined	0.163
r_chiral_restr	0.113
r_bond_refined_d	0.018
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3946
Nucleic Acid Atoms
Solvent Atoms	215
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.