5EFF | pdb_00005eff

Crystal structure of an aromatic mutant (F4A) of an alkali thermostable GH10 xylanase from Bacillus sp. NG-27

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	0.1M NaCl, 0.14M MgCl2, 0.05M Tris HCl pH 8.5, 15% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.62	α = 90
b = 67.71	β = 90
c = 181.54	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	IMAGE PLATE	MAR scanner 345 mm plate		2013-05-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	2.227	90.77	95.5	0.098	0.103	0.033	17.4	9.1	31730	31730

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.21	2.33	77.4		0.196	0.196	0.065	3.7	8.2	3685

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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		THROUGHOUT	2.23	90.77	30125	1555	97.01	0.1815	0.1785	0.19	0.2402	0.25	RANDOM	12.919

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]
0.6			0.08		-0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.057
r_dihedral_angle_4_deg	16.87
r_dihedral_angle_3_deg	14.565
r_dihedral_angle_1_deg	6.26
r_angle_other_deg	1.973
r_angle_refined_deg	1.593
r_mcangle_it	1.583
r_mcbond_it	0.912
r_mcbond_other	0.912
r_chiral_restr	0.086

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.057
r_dihedral_angle_4_deg	16.87
r_dihedral_angle_3_deg	14.565
r_dihedral_angle_1_deg	6.26
r_angle_other_deg	1.973
r_angle_refined_deg	1.593
r_mcangle_it	1.583
r_mcbond_it	0.912
r_mcbond_other	0.912
r_chiral_restr	0.086
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_gen_planes_other	0.006
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5771
Nucleic Acid Atoms
Solvent Atoms	117
Heterogen Atoms	5

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SCALA	data reduction
PHASER	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.