5EB8 | pdb_00005eb8

Crystal structure of aromatic mutant (F4W) of an alkali thermostable GH10 xylanase from Bacillus sp. NG-27

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2F8Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	8.5	293	0.1M NaCl, 120mM MgCl2, 0.1M Tris-HCl pH 8.5, 18% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.27	α = 90
b = 77.32	β = 90
c = 176.75	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	RIGAKU		2012-06-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU ULTRAX 18	1.54179

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	2.219	88.375	98.4	0.083	0.089	0.033	15.1	7.1	38071	38071

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	89.8		0.2	0.2	0.081	3.7	6.7	4956

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	2F8Q	2.22	88.375	36158	1841	99.08	0.1706	0.1684	0.18	0.2139	0.22	RANDOM	27.172

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]
2.74			1.43		-4.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.03
r_dihedral_angle_4_deg	15.295
r_dihedral_angle_3_deg	12.301
r_dihedral_angle_1_deg	5.786
r_mcangle_it	1.503
r_angle_refined_deg	1.228
r_mcbond_it	0.911
r_mcbond_other	0.911
r_angle_other_deg	0.783
r_chiral_restr	0.072

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.03
r_dihedral_angle_4_deg	15.295
r_dihedral_angle_3_deg	12.301
r_dihedral_angle_1_deg	5.786
r_mcangle_it	1.503
r_angle_refined_deg	1.228
r_mcbond_it	0.911
r_mcbond_other	0.911
r_angle_other_deg	0.783
r_chiral_restr	0.072
r_bond_refined_d	0.009
r_bond_other_d	0.006
r_gen_planes_refined	0.005
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5796
Nucleic Acid Atoms
Solvent Atoms	417
Heterogen Atoms	4

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.