2XVG | pdb_00002xvg

crystal structure of alpha-xylosidase (GH31) from Cellvibrio japonicus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2G3M	PDB ENTRY 2G3M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		25 % PEG MONOMETHYL ETHER 550 (PEG MME 550), 0.1 M BIS-TRIS (PH 7.0)

Crystal Properties
Matthews coefficient	Solvent content
3.59	65.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 156.193	α = 90
b = 156.193	β = 90
c = 227.759	γ = 120

Symmetry
Space Group	P 63 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 CCD	MIRRORS	2009-09-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29		ESRF	ID29

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	2.6	49.9	99.9	0.11	14.4	11		50969		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.74	100		0.81	2.7	11.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 2G3M	2.6	49.885	1.36	50969	2587	99.93	0.2065	0.2038	0.2043	0.259	0.2579

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.681
f_angle_d	1.156
f_chiral_restr	0.078
f_bond_d	0.009
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7577
Nucleic Acid Atoms
Solvent Atoms	103
Heterogen Atoms	23

Software

Software
Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALEPACK	data scaling
BALBES	phasing