7PSH

Crystal structure of beta-glucuronidase from Acidobacterium capsulatum at 1.24 Angstrom resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5G0M

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
2.43	49.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.865	α = 90
b = 44.149	β = 97.577
c = 136.277	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 PILATUS 6M-F		2019-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.911880	Diamond	I04-1

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	1.24	74.69	97.2	0.998	11.6	6.1		134306

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	1.26	1.26			0.794	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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5g0m	1.24	74.69	134258	6827	96.845	0.17	0.1686	0.1878	16.347

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]
-0.922		0.17	0.688		0.183

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.547
r_dihedral_angle_4_deg	17.424
r_dihedral_angle_3_deg	12.174
r_dihedral_angle_1_deg	6.315
r_lrange_it	4.923
r_lrange_other	4.85
r_scangle_it	3.763
r_scangle_other	3.762
r_scbond_it	2.563
r_scbond_other	2.562
r_angle_other_deg	2.405
r_mcangle_it	2.289
r_mcangle_other	2.289
r_angle_refined_deg	1.959
r_mcbond_it	1.6
r_mcbond_other	1.6
r_nbd_refined	0.232
r_symmetry_nbd_other	0.221
r_nbd_other	0.217
r_symmetry_xyhbond_nbd_refined	0.212
r_nbtor_refined	0.191
r_symmetry_nbd_refined	0.163
r_symmetry_xyhbond_nbd_other	0.121
r_xyhbond_nbd_refined	0.12
r_chiral_restr	0.103
r_symmetry_nbtor_other	0.083
r_bond_other_d	0.036
r_gen_planes_other	0.02
r_bond_refined_d	0.018
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3372
Nucleic Acid Atoms
Solvent Atoms	411
Heterogen Atoms	5

Software

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