7DFO | pdb_00007dfo

Crystal structure of glycoside hydrolase family 11 beta-xylanase from Streptomyces olivaceoviridis E-86 in complex with 4-O-methyl-alpha-D-glucuronopyranosyl xylotetraose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7DFM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.4	293	2.9 M sodium chloride, 0.1 M sodium citrate buffer pH 5.4

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 142.709	α = 90
b = 142.709	β = 90
c = 72.454	γ = 120

Symmetry
Space Group	P 32

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	PIXEL	DECTRIS EIGER X 16M		2019-02-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	0.9800	Photon Factory	BL-17A

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	100	99.3	0.165	17.9	8.7		110677

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	2	2.07			0.839	2.3

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7DFM	2	47.061	110646	5434	99.239	0.168	0.1651	0.17	0.2176	0.22	30.941

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]
0.856	0.428		0.856		-2.776

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.067
r_dihedral_angle_3_deg	13.709
r_dihedral_angle_4_deg	13.47
r_dihedral_angle_1_deg	8.316
r_lrange_it	5.281
r_lrange_other	5.28
r_scangle_it	4.161
r_scangle_other	4.161
r_mcangle_it	2.978
r_mcangle_other	2.978
r_scbond_it	2.845
r_scbond_other	2.844
r_mcbond_it	2.256
r_mcbond_other	2.256
r_angle_refined_deg	1.577
r_angle_other_deg	1.365
r_nbd_other	0.217
r_metal_ion_refined	0.206
r_nbd_refined	0.185
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.18
r_symmetry_nbd_refined	0.145
r_xyhbond_nbd_refined	0.144
r_symmetry_xyhbond_nbd_refined	0.113
r_symmetry_xyhbond_nbd_other	0.089
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.059
r_symmetry_metal_ion_refined	0.057
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13486
Nucleic Acid Atoms
Solvent Atoms	848
Heterogen Atoms	328

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
DENZO	data scaling
MOLREP	phasing