8I5O

Crystal structure of TxGH116 D593A acid/base mutant from Thermoanaerobacterium xylanolyticum

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	288	0.24 M AMMONIUM SULFATE, 21% PEG 3000, 0.1 M MES, PH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 178.199	α = 90
b = 54.376	β = 90
c = 83.378	γ = 90

Symmetry
Space Group	P 21 21 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	CCD	ADSC QUANTUM 315r		2014-10-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13B1	1.0	NSRRC	BL13B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	2.3	30	99.9	0.143	0.108	0.157	0.063	12.6	5.9		37034

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.38	99.7		0.658	0.603	0.732	0.317	0.777	2.4	5

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5BVU	2.3	30	34970	1779	99.49	0.1754	0.173	0.2228	RANDOM	33.299

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]
-0.32			0.08		0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.301
r_dihedral_angle_4_deg	16.178
r_dihedral_angle_3_deg	12.37
r_dihedral_angle_1_deg	6.08
r_angle_refined_deg	1.156
r_angle_other_deg	0.871
r_chiral_restr	0.07
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.301
r_dihedral_angle_4_deg	16.178
r_dihedral_angle_3_deg	12.37
r_dihedral_angle_1_deg	6.08
r_angle_refined_deg	1.156
r_angle_other_deg	0.871
r_chiral_restr	0.07
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6206
Nucleic Acid Atoms
Solvent Atoms	278
Heterogen Atoms	13

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data scaling
MOLREP	phasing
Coot	model building
PDB_EXTRACT	data extraction
HKL-2000	data reduction

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.