2Y6L | pdb_00002y6l

Xylopentaose binding X-2 engineered mutated CBM4-2 Carbohydrate Binding Module from a Thermostable Rhodothermus marinus Xylanase

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Y6K	PDB ENTRY 2Y6K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		1.2 M SODIUM CITRATE PH 6.4

Crystal Properties
Matthews coefficient	Solvent content
2.1	42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.9	α = 90
b = 49.48	β = 90
c = 62.49	γ = 90

Symmetry
Space Group	P 21 21 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	MARRESEARCH MAR165	MIRRORS	2008-09-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-2		MAX II	I911-2

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	1.28	30	96.9	0.06	15.9	4.8		38527		-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	1.28	1.31	94.9		0.56	3.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2Y6K	1.28	30	36600	1927	92	0.135	0.132		0.17	0.183	RANDOM

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
38	1256	1531.7

RMS Deviations
Key	Refinement Restraint Deviation
s_approx_iso_adps	0.083
s_zero_chiral_vol	0.069
s_non_zero_chiral_vol	0.065
s_anti_bump_dis_restr	0.058
s_from_restr_planes	0.033
s_similar_adp_cmpnt	0.032
s_angle_d	0.031
s_bond_d	0.011
s_rigid_bond_adp_cmpnt	0.004
s_similar_dist

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1265
Nucleic Acid Atoms
Solvent Atoms	227
Heterogen Atoms	48

Software

Software
Software Name	Purpose
SHELXL-97	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	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.