6SXS | pdb_00006sxs

GH54 a-l-arabinofuranosidase soaked with cyclic sulfate inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1WD3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	293	2:1 protein:well solution. 0.1 M pH 4.5 sodium acetate buffer, 60% PEG400, 0.3 M (NH4)2SO4

Crystal Properties
Matthews coefficient	Solvent content
4	34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.136	α = 90
b = 111.136	β = 90
c = 342.742	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 EIGER2 X 16M		2019-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	1.859	84.059	100	0.128	0.133	0.039	0.999	10.2	12.1		68786

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.86	1.89	100		5.32	5.54	1.53	0.44	0.5	12.8

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1WD3	1.859	84.059	68786	3338	99.73	0.183	0.1817	0.19	0.215	0.22	40.242

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]
0.885	0.443		0.885		-2.872

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.2
r_dihedral_angle_4_deg	21.509
r_dihedral_angle_3_deg	11.758
r_dihedral_angle_1_deg	8.225
r_lrange_it	5.61
r_lrange_other	5.591
r_scangle_it	5.198
r_scangle_other	5.197
r_scbond_it	4.036
r_scbond_other	4.035
r_mcangle_other	3.688
r_mcangle_it	3.686
r_mcbond_it	3.102
r_mcbond_other	3.059
r_angle_refined_deg	1.768
r_angle_other_deg	1.463
r_symmetry_nbd_refined	0.311
r_nbd_other	0.216
r_nbd_refined	0.196
r_symmetry_nbd_other	0.18
r_nbtor_refined	0.174
r_xyhbond_nbd_refined	0.129
r_symmetry_xyhbond_nbd_refined	0.122
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.076
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3568
Nucleic Acid Atoms
Solvent Atoms	235
Heterogen Atoms	131

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing