3CU9 | pdb_00003cu9

High resolution crystal structure of 1,5-alpha-L-arabinanase from Geobacillus Stearothermophilus

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1WL7	PDB ENTRY 1WL7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	295	1.7M Lithium Sulfate, 0.1M Tris buffer pH 7.5, 15% (v/v) Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.141	α = 90
b = 89.579	β = 90
c = 76.041	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	MARMOSAIC 225 mm CCD		2005-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.978578	SLS	X10SA

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	1.06	50	98.5	0.096	0.096	16.7	14.6	132831	130844			6.1

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	1.06	1.08	77.7		0.258	0.235		7.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	AB INITIO	FREE R	PDB ENTRY 1WL7	1.06	30	124263	124263	6547	93.4	0.1475	0.1472	0.1472	0.14	0.1761	0.15	RANDOM	14.5

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
396		2926.7

RMS Deviations
Key	Refinement Restraint Deviation
s_non_zero_chiral_vol	0.095
s_zero_chiral_vol	0.093
s_similar_adp_cmpnt	0.039
s_from_restr_planes	0.0338
s_anti_bump_dis_restr	0.033
s_angle_d	0.031
s_bond_d	0.015
s_rigid_bond_adp_cmpnt	0.005
s_similar_dist
s_approx_iso_adps

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2523
Nucleic Acid Atoms
Solvent Atoms	398
Heterogen Atoms	7

Software

Software
Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	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.