8UWT | pdb_00008uwt

A X-ray Crystallographic Structure Model of a Glycoside Hydrolase (GH) Family 39 (GH39)-like Enzyme Encoded within a Xylan Utilization Locus of the pSOL1 Megaplasmid of Clostridium acetobutylicum

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5U22

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Hampton Research PEGRx HT: Condition 80 (G8): 0.2 M Sodium Formate, 0.1 M BICINE pH 8.5, 20% PEG5000 MME. This condition was extensively refined and the crystal which generated the data for this deposit consisted of the same, but had pH adjusted to 8.3.

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.407	α = 90
b = 88.245	β = 90
c = 106.593	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	105	PIXEL	DECTRIS PILATUS3 2M	Rhodium coated silicon single crystal	2018-03-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.55	100	94.3	0.155	0.162	0.047	0.995	4.7	11		96886

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.61	60.6		1.53	1.72	0.751	0.277		3.8

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	1.55	35.89	78644	4294	80.48	0.14429	0.14238	0.1562	0.17987	0.1896	RANDOM	17.324

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]
-0.31			-0.25		0.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.596
r_dihedral_angle_4_deg	19.689
r_dihedral_angle_3_deg	12.399
r_dihedral_angle_1_deg	6.997
r_long_range_B_refined	5.726
r_long_range_B_other	5.576
r_scangle_other	3.193
r_scbond_it	2.196
r_scbond_other	2.058
r_mcangle_other	1.92
r_mcangle_it	1.919
r_angle_refined_deg	1.539
r_angle_other_deg	1.458
r_mcbond_it	1.304
r_mcbond_other	1.304
r_chiral_restr	0.08
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6250
Nucleic Acid Atoms
Solvent Atoms	872
Heterogen Atoms	130

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
HKL-3000	data reduction
PHASER	phasing