6JDT | pdb_00006jdt

Crystal structure of GH10 family xylanase XynAF1 from Aspergillus fumigatus Z5

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1M MES pH6.5, 25%(w/v) PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.606	α = 73.86
b = 57.575	β = 80.39
c = 65.088	γ = 68.35

Symmetry
Space Group	P 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	CCD	ADSC QUANTUM 315r		2016-10-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.979	SSRF	BL17U1

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	1.68	50	96.1	0.105	12.59	2.7		62812			10.16

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	1.68	1.71	93.4		0.447	7.3	2.8

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	1.68	50	59733	3079	96.06	0.1374	0.1358	0.1495	0.1678	0.1771	RANDOM	11.518

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]
0.17	-0.08	0.75	-0.06	-0.21	-0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.656
r_dihedral_angle_3_deg	11.799
r_dihedral_angle_1_deg	6.844
r_dihedral_angle_4_deg	3.912
r_angle_refined_deg	1.966
r_angle_other_deg	1.094
r_chiral_restr	0.135
r_bond_refined_d	0.021
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4870
Nucleic Acid Atoms
Solvent Atoms	450
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing