2IJR | pdb_00002ijr

Crystal structure of a protein api92 from Yersinia pseudotuberculosis, Pfam DUF1281

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	0.5M Magnesium formate, 0.1M Bis Tris, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.14	60.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.656	α = 90
b = 88.656	β = 90
c = 218.227	γ = 90

Symmetry
Space Group	I 41 2 2

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 315		2006-09-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	.9792	NSLS	X29A

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	2.7	40	57	0.134	0.133	9.6	3.8		11612	2	2	40.2

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)
	2.7	2.8	51.9		0.293	0.269	2.7	1.9	1198

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 (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	SAD	THROUGHOUT	2.7	20	10960	577	93.33	0.22747	0.22747	0.22476	0.22	0.27917	0.28	RANDOM	15.158

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]
0.12			0.12		-0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.94
r_dihedral_angle_4_deg	24.548
r_dihedral_angle_3_deg	23.167
r_dihedral_angle_1_deg	22.029
r_scangle_it	3.762
r_angle_refined_deg	2.67
r_scbond_it	2.327
r_mcangle_it	1.624
r_mcbond_it	0.99
r_nbtor_refined	0.331

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.94
r_dihedral_angle_4_deg	24.548
r_dihedral_angle_3_deg	23.167
r_dihedral_angle_1_deg	22.029
r_scangle_it	3.762
r_angle_refined_deg	2.67
r_scbond_it	2.327
r_mcangle_it	1.624
r_mcbond_it	0.99
r_nbtor_refined	0.331
r_nbd_refined	0.276
r_symmetry_vdw_refined	0.247
r_chiral_restr	0.232
r_xyhbond_nbd_refined	0.212
r_symmetry_hbond_refined	0.178
r_bond_refined_d	0.019
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2241
Nucleic Acid Atoms
Solvent Atoms	44
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXS	phasing

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.