8EKN | pdb_00008ekn

Co-crystal structure of Chaetomium glucosidase with compound 15

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	58.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.875	α = 90
b = 179.332	β = 90
c = 179.833	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 PILATUS 6M		2021-06-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.9794	SSRL	BL9-2

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	2.29	46.83	99.36	0.11	0.03868	0.998	9.75	8.9		97615

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	2.29	2.375	94.6		0.9202	0.3355	0.797	1.61	8.4

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	2.29	46.83	92672	4944	99.38	0.1905	0.1881	0.19	0.2344	0.24	RANDOM	38.904

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]
2.25			0.11		-2.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.8
r_dihedral_angle_4_deg	18.13
r_dihedral_angle_3_deg	16.115
r_dihedral_angle_1_deg	7.36
r_angle_refined_deg	1.743
r_angle_other_deg	1.363
r_chiral_restr	0.085
r_gen_planes_refined	0.009
r_bond_refined_d	0.008
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.8
r_dihedral_angle_4_deg	18.13
r_dihedral_angle_3_deg	16.115
r_dihedral_angle_1_deg	7.36
r_angle_refined_deg	1.743
r_angle_other_deg	1.363
r_chiral_restr	0.085
r_gen_planes_refined	0.009
r_bond_refined_d	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12149
Nucleic Acid Atoms
Solvent Atoms	409
Heterogen Atoms	180

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.