4QCF | pdb_00004qcf

Crystal structure of N-terminal mutant (V1A) 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, 0.09M MgCl2, 0.05M Tris HCl pH 8.5, 15% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.57	α = 90
b = 80.12	β = 110.81
c = 69.9	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	IMAGE PLATE	MAR scanner 345 mm plate	MIRRORS	2012-10-13	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)	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	2.26	65.34	96.3	0.039	25.5	5.2	17095	17095

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	2.26	2.38	94.5		0.153	0.153	0.081	4.9	5.1	2419

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.26	26.78	17094	877	95.88	0.177	0.1745	0.18	0.2248	0.23	RANDOM	26.355

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]
-1.25		-1.22	0.06		1.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.89
r_dihedral_angle_4_deg	15.677
r_dihedral_angle_3_deg	11.986
r_dihedral_angle_1_deg	5.444
r_angle_refined_deg	0.955
r_angle_other_deg	0.718
r_mcangle_it	0.58
r_mcbond_it	0.326
r_mcbond_other	0.326
r_chiral_restr	0.055

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.89
r_dihedral_angle_4_deg	15.677
r_dihedral_angle_3_deg	11.986
r_dihedral_angle_1_deg	5.444
r_angle_refined_deg	0.955
r_angle_other_deg	0.718
r_mcangle_it	0.58
r_mcbond_it	0.326
r_mcbond_other	0.326
r_chiral_restr	0.055
r_bond_refined_d	0.005
r_bond_other_d	0.005
r_gen_planes_refined	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2893
Nucleic Acid Atoms
Solvent Atoms	202
Heterogen Atoms	5

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
MOSFLM	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.