4N2R | pdb_00004n2r

Crystal Structure of the alpha-L-arabinofuranosidase UmAbf62A from Ustilago maydis in complex with L-arabinofuranose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4N1I	PDB entry 4N1I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	285	20% (w/v) PEG 3350 0.2 M Sodium phosphate 0.05 M Na Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 285.0K

Crystal Properties
Matthews coefficient	Solvent content
1.82	32.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.08	α = 90
b = 66.07	β = 90
c = 68.1	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 210		2012-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.93340	ESRF	ID14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	1.2	50	95.9	0.026	35	4.3	85293	81763	1	-3	12.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.2	1.23	89.9		0.143	9.35	4.2	5597

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	PDB entry 4N1I	1.2	47.42	1	81763	77664	4098	95.85	0.10118	0.09965	0.12	0.13016	0.14	RANDOM	10.908

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]
-0.01			0.04		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	35.944
r_dihedral_angle_2_deg	29.774
r_dihedral_angle_4_deg	25.815
r_dihedral_angle_3_deg	11.796
r_sphericity_bonded	10.793
r_dihedral_angle_1_deg	7.884
r_rigid_bond_restr	6.109
r_long_range_B_refined	4.768
r_long_range_B_other	3.877
r_scangle_other	3.328
r_scbond_it	2.813
r_scbond_other	2.809
r_mcbond_it	2.692
r_mcangle_other	2.679
r_mcangle_it	2.671
r_mcbond_other	2.669
r_angle_refined_deg	2.117
r_angle_other_deg	0.98
r_chiral_restr	0.128
r_bond_refined_d	0.022
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.002
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	2376
Nucleic Acid Atoms
Solvent Atoms	438
Heterogen Atoms	29

Software

Software
Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling