3LM7 | pdb_00003lm7

Crystal Structure of DUF1341 representative, from Yersinia enterocolitica subsp. enterocolitica 8081

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.6	289	0.15M potassium bromide, 30% w/v polyethylene glycol monomethyl ether 2000 (Hampton Index #96), pH 7.60, VAPOR DIFFUSION, SITTING DROP, temperature 289.0K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.947	α = 90
b = 60.453	β = 90
c = 159.119	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	100	CCD	ADSC QUANTUM 210r	Si (111) double crystal monochromator	2009-11-18	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97915, 0.97942	APS	19-BM

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	1.9	100	93	0.065		9.6	755369	702493	2

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)
	1.9	1.95	95		0.272	0.248	6.4	5.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	1.9	79.56	36623	1932	99.18	0.13789	0.13498	0.1445	0.19173	0.1952	RANDOM	13.943

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]
0.06			-0.15		0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.626
r_dihedral_angle_4_deg	18.548
r_dihedral_angle_3_deg	13.956
r_dihedral_angle_1_deg	6.096
r_scangle_it	5.3
r_scbond_it	3.323
r_mcangle_it	1.902
r_angle_refined_deg	1.858
r_mcbond_it	1.156
r_chiral_restr	0.152

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.626
r_dihedral_angle_4_deg	18.548
r_dihedral_angle_3_deg	13.956
r_dihedral_angle_1_deg	6.096
r_scangle_it	5.3
r_scbond_it	3.323
r_mcangle_it	1.902
r_angle_refined_deg	1.858
r_mcbond_it	1.156
r_chiral_restr	0.152
r_bond_refined_d	0.025
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3725
Nucleic Acid Atoms
Solvent Atoms	720
Heterogen Atoms	3

Software

Software
Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

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.