6VHO | pdb_00006vho

Glycoside hydrolase family 16 endo-glucanase from Bacteroides ovatus in complex with G4G4G3G-NHCOCH2Br

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.1 M succinic acid pH 7.2, 15 % (w/v) PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 168.58	α = 90
b = 61.15	β = 93.608
c = 49.411	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	PIXEL	DECTRIS EIGER X 16M		2019-03-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.0332	APS	23-ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.148	84.123	96	0.993	7	1.8		27458

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.44			0.76

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-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5NBO	2.148	84.123	27458	1311	99.507	0.187	0.1857	0.2067	28.927

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]
1.798		1.226	-0.576		-1.365

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.626
r_dihedral_angle_3_deg	13.921
r_dihedral_angle_4_deg	9.73
r_dihedral_angle_1_deg	8.497
r_lrange_it	4.295
r_lrange_other	4.269
r_scangle_it	3.273
r_scangle_other	3.267
r_angle_other_deg	2.482
r_mcangle_other	2.361
r_mcangle_it	2.36
r_scbond_it	2.043
r_scbond_other	2.037
r_mcbond_it	1.543
r_mcbond_other	1.538
r_angle_refined_deg	1.388
r_symmetry_nbd_other	0.206
r_nbd_refined	0.183
r_nbtor_refined	0.163
r_nbd_other	0.15
r_xyhbond_nbd_refined	0.148
r_symmetry_xyhbond_nbd_refined	0.101
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.056
r_symmetry_nbd_refined	0.047
r_bond_other_d	0.036
r_gen_planes_other	0.007
r_bond_refined_d	0.006
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3770
Nucleic Acid Atoms
Solvent Atoms	199
Heterogen Atoms	37

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Coot	model building
PHASER	phasing
XSCALE	data scaling