8OHU | pdb_00008ohu

Crystal structure of Beta-glucuronidase from Acidobacterium capsulatum in complex with glucuronic acid configured isofagamine

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.5 M AmSO4 1 M LiSO4 0.1 M Trisodium Citrate

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.046	α = 90
b = 44.669	β = 97.605
c = 137.173	γ = 90

Symmetry
Space Group	I 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 EIGER2 X 16M		2021-02-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.979499	Diamond	I04

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	1.25	42.44	99	0.998	10.2	6.2		136682

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	1.25	1.27			0.882

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.25	42.44	136675	6866	98.942	0.165	0.164	0.17	0.184	0.17	14.323

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]
-0.448		0.55	1.049		-0.722

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.183
r_dihedral_angle_4_deg	18.799
r_dihedral_angle_3_deg	12.64
r_dihedral_angle_1_deg	6.291
r_lrange_it	5.114
r_lrange_other	5.093
r_scangle_it	3.985
r_scangle_other	3.984
r_scbond_it	2.692
r_scbond_other	2.691
r_mcangle_it	2.222
r_mcangle_other	2.222
r_angle_refined_deg	1.931
r_angle_other_deg	1.642
r_mcbond_it	1.504
r_mcbond_other	1.498
r_chiral_restr_other	0.431
r_symmetry_nbd_refined	0.235
r_nbd_refined	0.219
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.184
r_symmetry_xyhbond_nbd_refined	0.183
r_nbd_other	0.178
r_xyhbond_nbd_refined	0.167
r_chiral_restr	0.105
r_symmetry_nbtor_other	0.091
r_symmetry_xyhbond_nbd_other	0.06
r_bond_refined_d	0.015
r_gen_planes_refined	0.011
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3453
Nucleic Acid Atoms
Solvent Atoms	357
Heterogen Atoms	11

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing