Experiment: 3MS8

Enzyme-Substrate interactions of IXT6, the intracellular xylanase of G. stearothermophilus.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Q8X	PDB ENTRY 2Q8X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.1M sodium cacodylate pH=6.5, 1.9M soduim acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.47	64.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 169.389	α = 90
b = 80.081	β = 91.5
c = 79.026	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	100	CCD	ADSC QUANTUM 4r		2002-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.939	ESRF	ID14-4

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	1.7	19.89	97	0.05	15.3	2.88	319380	110960		15.3	20.4

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	1.7	1.73	88.5		0.161	4.7	1.76	5019

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	Its 2Q8X only one point mutation, using its phases doing rigid and annealing	THROUGHOUT	PDB ENTRY 2Q8X	1.7	19.89	107077	107077	5384	92.9	0.196	0.2076	0.209	0.2199	RANDOM	30.1

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]
-13.02		-2.02	17.81		-4.79

RMS Deviations
Key	Refinement Restraint Deviation
DIHEDRAL ANGLES	22.1
BOND ANGLES	1.3
IMPROPER ANGLES	0.8
BOND LENGTHS	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5385
Nucleic Acid Atoms
Solvent Atoms	443
Heterogen Atoms	38

Software

Software
Software Name	Purpose
DENZO	data reduction
CNS	refinement
SCALEPACK	data scaling
CNS	phasing