6F1J | pdb_00006f1j

Structure of a Talaromyces pinophilus GH62 Arabinofuranosidase in complex with AraDNJ at 1.25A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3WMY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	30% PEG2K MME, 0.2M KBr

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.827	α = 90
b = 88.978	β = 95.22
c = 72.663	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 6M-F		2016-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.93	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.25	33.52	98	0.04	13.1	3.1		149344

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.25	1.27	91		0.28		2.1

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3wmy	1.25	33.52	141792	7516	97.68	0.12055	0.11972	0.12	0.13588	0.14	RANDOM	7.871

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]
-0.34		0.13	-0.04		0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.501
r_dihedral_angle_4_deg	23.495
r_sphericity_free	20.668
r_dihedral_angle_3_deg	10.16
r_dihedral_angle_1_deg	7.771
r_sphericity_bonded	5.291
r_long_range_B_refined	2.157
r_long_range_B_other	1.582
r_angle_refined_deg	1.499
r_rigid_bond_restr	1.321
r_scangle_other	1.101
r_mcangle_it	1.022
r_mcangle_other	1.022
r_angle_other_deg	0.975
r_scbond_it	0.91
r_scbond_other	0.908
r_mcbond_it	0.771
r_mcbond_other	0.77
r_chiral_restr	0.104
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4540
Nucleic Acid Atoms
Solvent Atoms	658
Heterogen Atoms	50

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
MOLREP	phasing
xia2	data reduction