3KL5 | pdb_00003kl5

Structure Analysis of a Xylanase From Glycosyl Hydrolase Family Thirty: Carbohydrate Ligand Complexes Reveal this Family of Enzymes Unique Mechanism of Substrate Specificity and Recognition

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3KL0	PDB ENTRY 3KL0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294.6	200 mM sodium tartrate, 200 mM sodium malonate, pH 7.0, 19% PEG3350 Crystal was soaked in mother liquor with cryoprotectent and aldotetrauronic acid, VAPOR DIFFUSION, SITTING DROP, temperature 294.6K

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 137.723	α = 90
b = 194.008	β = 90
c = 65.707	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	105	CCD	RAYONIX MX-325		2009-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.97946	SSRL	BL12-2

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	2.59	50	97.9	0.086	10.6	6.6		54718

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)
	2.59	2.68	85.4		0.892		3.2	4686

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3KL0	2.59	50	54602	2778	97.55	0.243	0.241	0.24	0.29	0.28	RANDOM	73.226

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]
-0.55			2.66		-2.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.126
r_dihedral_angle_4_deg	20.197
r_dihedral_angle_3_deg	16.742
r_dihedral_angle_1_deg	6
r_scangle_it	2.084
r_angle_refined_deg	1.246
r_scbond_it	1.208
r_mcangle_it	1.004
r_mcbond_it	0.526
r_chiral_restr	0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.126
r_dihedral_angle_4_deg	20.197
r_dihedral_angle_3_deg	16.742
r_dihedral_angle_1_deg	6
r_scangle_it	2.084
r_angle_refined_deg	1.246
r_scbond_it	1.208
r_mcangle_it	1.004
r_mcbond_it	0.526
r_chiral_restr	0.08
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12259
Nucleic Acid Atoms
Solvent Atoms	47
Heterogen Atoms	127

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
Web-Ice	data collection

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.