3OG3 | pdb_00003og3

Crystal structure of an artificial thermostable (BA)8-barrel protein from identical half barrels

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1THF	PDB ENTRY 1THF (Amino acids 99-219) dimer

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	0.2 M ammonium sulfate, 18% PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.76	29.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.374	α = 90
b = 82.086	β = 90.11
c = 74.511	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	123	CCD	OXFORD RUBY CCD	mirrors	2009-12-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	OXFORD DIFFRACTION ENHANCE ULTRA	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.08	14.7	99.6	0.052	18.58		11304	11304	1	1	26

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.04	2.14	96.8		0.168	3.8	2.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1THF (Amino acids 99-219) dimer	2.08	14.65	1	11260	10719	584	99.63	0.166	0.15194	0.14953	0.15	0.19591	0.2	RANDOM	17.478

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]
0.02		-0.08	-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.184
r_dihedral_angle_4_deg	13.474
r_dihedral_angle_3_deg	11.481
r_dihedral_angle_1_deg	6.33
r_scangle_it	5.278
r_scbond_it	3.343
r_mcangle_it	2.345
r_angle_refined_deg	2.006
r_mcbond_it	1.375
r_chiral_restr	0.139

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.184
r_dihedral_angle_4_deg	13.474
r_dihedral_angle_3_deg	11.481
r_dihedral_angle_1_deg	6.33
r_scangle_it	5.278
r_scbond_it	3.343
r_mcangle_it	2.345
r_angle_refined_deg	2.006
r_mcbond_it	1.375
r_chiral_restr	0.139
r_bond_refined_d	0.025
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1836
Nucleic Acid Atoms
Solvent Atoms	173
Heterogen Atoms	12

Software

Software
Software Name	Purpose
CrysalisPro	data collection
Oxford	data collection
PHASER	phasing
REFMAC	refinement
CrysalisPro	data reduction
Oxford	data reduction
SCALA	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.