5GYG | pdb_00005gyg

Crystal structure of ENZbleach xylanase T28C+T60C mutant with three N-teminal residue truncation

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5GV1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		298	PEG 3350, 0.1 M tri-sodium acetate pH 4.5, 0.1 M Bis-Tris pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.253	α = 90
b = 70.886	β = 90.23
c = 85.254	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	ADSC QUANTUM 315		2015-07-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13B1	1	NSRRC	BL13B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.74	50.01	93.2	0.032	22.9	2.1		48098

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	1.74	1.8	82.1		0.095	0.978		1.8

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	5GV1	1.74	50	45542	2467	92.86	0.1768	0.1744	0.17	0.2221	0.22	RANDOM	17.024

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]
-0.61		-0.24	0.57		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.069
r_dihedral_angle_4_deg	14.559
r_dihedral_angle_3_deg	12.309
r_dihedral_angle_1_deg	6.961
r_mcangle_it	1.415
r_angle_refined_deg	1.379
r_scbond_it	1.171
r_mcbond_it	0.872
r_chiral_restr	0.094
r_bond_refined_d	0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.069
r_dihedral_angle_4_deg	14.559
r_dihedral_angle_3_deg	12.309
r_dihedral_angle_1_deg	6.961
r_mcangle_it	1.415
r_angle_refined_deg	1.379
r_scbond_it	1.171
r_mcbond_it	0.872
r_chiral_restr	0.094
r_bond_refined_d	0.011
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4300
Nucleic Acid Atoms
Solvent Atoms	728
Heterogen Atoms

Software

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

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.