8ANX | pdb_00008anx

E329A Mutant Thermogutta terrifontis endoglucanase catalytic domain with C-linker from glycoside hydrolase family 5 (TtEnd5A-CDC-E329A)

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8AG9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293.15	0.2M NH4Cl and 20%W/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.39	α = 90
b = 69.59	β = 90
c = 81.92	γ = 90

Symmetry
Space Group	P 21 21 21

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 12M		2021-09-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.13	69.59	96.8	0.045	0.047	0.013	1	18.9	11.6		125321			13.69

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.13	1.16	75.2		1.646	0.392		4.6

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	8AG9	1.2	69.59	108042	5308	99.712	0.121	0.1199	0.12	0.1484	0.15	16.638

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]
-0.468			-0.339		0.808

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.245
r_dihedral_angle_4_deg	19.653
r_dihedral_angle_3_deg	10.815
r_dihedral_angle_1_deg	6.407
r_lrange_it	2.671
r_lrange_other	2.336
r_scangle_other	1.947
r_scangle_it	1.945
r_scbond_it	1.571
r_scbond_other	1.569
r_angle_other_deg	1.5
r_angle_refined_deg	1.436
r_mcangle_other	1.354
r_mcangle_it	1.353
r_rigid_bond_restr	1.19
r_mcbond_it	1.004
r_mcbond_other	0.999
r_symmetry_xyhbond_nbd_refined	0.441
r_nbd_refined	0.224
r_nbd_other	0.196
r_symmetry_nbd_other	0.179
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.148
r_symmetry_nbd_refined	0.139
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.075
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	2719
Nucleic Acid Atoms
Solvent Atoms	375
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing