6SXR | pdb_00006sxr

E221Q mutant of GH54 a-l-arabinofuranosidase soaked with 4-nitrophenyl a-l-arabinofuranoside

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, 0.4 M Li2SO4

Crystal Properties
Matthews coefficient	Solvent content
	34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.97	α = 90
b = 111.97	β = 90
c = 341.39	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		2019-07-19	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)	Rrim 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	1.64	93.28	98.2	0.129	1	12.5	12.6		99211

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.64	1.67	97		2.319	0.5	1	12.2

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1WD3	1.64	93.28	99210	5141	98.143	0.161	0.1596	0.17	0.181	0.19	Random selection	26.156

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]
0.44	0.22		0.44		-1.427

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.402
r_dihedral_angle_4_deg	20.765
r_dihedral_angle_3_deg	10.73
r_dihedral_angle_1_deg	7.562
r_lrange_it	5.45
r_lrange_other	5.349
r_scangle_it	4.822
r_scangle_other	4.754
r_scbond_it	3.396
r_scbond_other	3.362
r_angle_other_deg	2.538
r_mcangle_other	2.491
r_mcangle_it	2.487
r_mcbond_it	2.013
r_mcbond_other	1.935
r_angle_refined_deg	1.873
r_symmetry_xyhbond_nbd_refined	0.501
r_symmetry_nbd_refined	0.306
r_symmetry_nbd_other	0.216
r_nbd_refined	0.206
r_nbd_other	0.193
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.121
r_chiral_restr	0.086
r_symmetry_nbtor_other	0.086
r_bond_other_d	0.037
r_gen_planes_other	0.017
r_bond_refined_d	0.014
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3572
Nucleic Acid Atoms
Solvent Atoms	352
Heterogen Atoms	260

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
DIALS	data scaling
PHASER	phasing