7DFN | pdb_00007dfn

Crystal structure of glycoside hydrolase family 11 beta-xylanase from Streptomyces olivaceoviridis E-86 in complex with alpha-L-arabinofuranosyl xylotetraose

X-RAY DIFFRACTION

---

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
2.08	40.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 134.233	α = 90
b = 134.233	β = 90
c = 72.235	γ = 120

Symmetry
Space Group	P 32 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	95	PIXEL	DECTRIS PILATUS3 2M		2018-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0000	Photon Factory	AR-NW12A

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	99.8	0.257	11.3	17.4		50743

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	2.05			1.11	2.2

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7DFM	2	49.217	50712	2660	99.768	0.167	0.1649	0.17	0.2093	0.22	ramdom	21.721

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]
0.681	0.34		0.681		-2.209

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.8
r_dihedral_angle_4_deg	16.018
r_dihedral_angle_3_deg	13.096
r_dihedral_angle_1_deg	8.542
r_lrange_it	4.33
r_lrange_other	4.307
r_scangle_it	3.111
r_scangle_other	3.111
r_mcangle_it	2.173
r_mcangle_other	2.173
r_scbond_it	2.041
r_scbond_other	2.04
r_angle_refined_deg	1.597
r_mcbond_it	1.527
r_mcbond_other	1.523
r_angle_other_deg	1.364
r_symmetry_nbd_refined	0.205
r_nbd_other	0.199
r_symmetry_xyhbond_nbd_refined	0.182
r_nbtor_refined	0.179
r_symmetry_nbd_other	0.178
r_nbd_refined	0.177
r_xyhbond_nbd_refined	0.173
r_metal_ion_refined	0.104
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.061
r_symmetry_xyhbond_nbd_other	0.016
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	5965
Nucleic Acid Atoms
Solvent Atoms	451
Heterogen Atoms	198

Software

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