6UAQ | pdb_00006uaq

Crystal structure of a GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei (AmGH128_I)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	291	sodium acetate 0.1 M sodium chloride 1.5 M

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.35	α = 90
b = 78.643	β = 101.62
c = 46.183	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	PIXEL	DECTRIS PILATUS 2M		2016-11-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	1.033140	LNLS	W01B-MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.15	45.28	94	0.998	11.51	2.35		171671

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.15	1.22			0.808

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MIRAS	THROUGHOUT	1.15	45.28	86795	4403	98.76	0.1506	0.15	0.15	0.1618	0.16	RANDOM	12.728

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]
0.56		0.42	-0.58		-0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.694
r_dihedral_angle_4_deg	11.925
r_dihedral_angle_3_deg	10.279
r_dihedral_angle_1_deg	6.98
r_mcangle_it	4.221
r_mcbond_it	3.668
r_mcbond_other	3.251
r_angle_other_deg	2.44
r_angle_refined_deg	2.097
r_chiral_restr	0.132

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.694
r_dihedral_angle_4_deg	11.925
r_dihedral_angle_3_deg	10.279
r_dihedral_angle_1_deg	6.98
r_mcangle_it	4.221
r_mcbond_it	3.668
r_mcbond_other	3.251
r_angle_other_deg	2.44
r_angle_refined_deg	2.097
r_chiral_restr	0.132
r_bond_other_d	0.036
r_gen_planes_other	0.022
r_bond_refined_d	0.018
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1813
Nucleic Acid Atoms
Solvent Atoms	355
Heterogen Atoms	19

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
SHELXDE	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.