8E3J | pdb_00008e3j

Co-crystal structure of Chaetomium glucosidase with compound 4

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7T6W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	297	0.1 Bis Tris pH 6.5, 1.6-2.0 M Ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.93	58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.207	α = 90
b = 179.208	β = 90
c = 180.59	γ = 90

Symmetry
Space Group	I 2 2 2

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 PILATUS3 6M		2021-03-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.9793	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.71	46.91	99.52	0.2304	0.1	0.976	6.53	6.3		59581

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.71	2.807	97.28		1.5	0.6945	0.849	1.22	5.8

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 (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	7T6W	2.71	46.91	56575	3039	99.46	0.1965	0.1939	0.2	0.2438	0.25	RANDOM	54.351

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]
3.37			1.83		-5.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.717
r_dihedral_angle_3_deg	18.036
r_dihedral_angle_4_deg	17.15
r_dihedral_angle_1_deg	7.546
r_angle_refined_deg	1.511
r_angle_other_deg	1.251
r_chiral_restr	0.069
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.717
r_dihedral_angle_3_deg	18.036
r_dihedral_angle_4_deg	17.15
r_dihedral_angle_1_deg	7.546
r_angle_refined_deg	1.511
r_angle_other_deg	1.251
r_chiral_restr	0.069
r_bond_refined_d	0.007
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	12070
Nucleic Acid Atoms
Solvent Atoms	29
Heterogen Atoms	186

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.