8AH3 | pdb_00008ah3

DG04279 glycoside hydrolase family 172

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	100 mM MOPS/HEPES pH 7.5, 20 mM 1,6-Hexanediol; 20 mM 1-Butanol 20 mM 1,2-Propanediol; 20 mM 2-Propanol; 20 mM 1,4-Butanediol; 20 mM 1,3-Propanedioalcohol, 20 % Etylene Glycol and 10 % PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.15	α = 90
b = 89.15	β = 90
c = 289.32	γ = 120

Symmetry
Space Group	H 3 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		2020-08-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9786	Diamond	I24

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	1.4	68.112	99.9	0.078	0.086	0.036	0.999	12.7	10.2		87401

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	1.4	1.42			0.412		6.6

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	4KQ7	1.4	68.112	87400	4427	99.921	0.163	0.1622	0.17	0.1839	0.19	24.541

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]
0.865	0.432		0.865		-2.805

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.712
r_dihedral_angle_3_deg	13.062
r_dihedral_angle_2_deg	12.547
r_dihedral_angle_1_deg	7.685
r_lrange_it	5.223
r_lrange_other	5.174
r_scangle_it	4.584
r_scangle_other	4.584
r_scbond_it	3.162
r_scbond_other	3.161
r_mcangle_other	2.498
r_mcangle_it	2.497
r_mcbond_it	2.049
r_mcbond_other	2.009
r_angle_refined_deg	1.703
r_angle_other_deg	0.606
r_symmetry_nbd_refined	0.303
r_nbd_refined	0.208
r_nbd_other	0.197
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.131
r_symmetry_xyhbond_nbd_refined	0.115
r_chiral_restr	0.094
r_symmetry_metal_ion_refined	0.092
r_metal_ion_refined	0.087
r_symmetry_nbtor_other	0.083
r_gen_planes_refined	0.012
r_bond_refined_d	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3043
Nucleic Acid Atoms
Solvent Atoms	208
Heterogen Atoms	4

Software

Software
Software Name	Purpose
XDS	data scaling
xia2	data scaling
pointless	data scaling
Aimless	data scaling
PHASER	phasing
Coot	model building
BUCCANEER	model building
MolProbity	model building
REFMAC	refinement
XDS	data reduction