7DIF | pdb_00007dif

GH127 beta-L-arabinofuranosidase HypBA1 covalently complexed with beta-L-arabinofuranose-configured cyclophellitol at 1.75-angstrom resolution

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.1 M MES-NaOH (pH 6.5), 0.7 M sodium citrate

Crystal Properties
Matthews coefficient	Solvent content
3.01	59.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.714	α = 90
b = 77.714	β = 90
c = 252.094	γ = 120

Symmetry
Space Group	P 32 2 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 2M-F		2020-11-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NE3A	1.000	Photon Factory	AR-NE3A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.75	46.05	100	0.083	0.039	0.999	10.8	9.9		90295			34.85

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.78	100		3.325	1.527	0.67		10.1

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	3WKX	1.75	46.05	85691	4482	99.96	0.2176	0.2162	0.2218	0.2433	0.2497	RANDOM	42.661

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]
1.27	0.64		1.27		-4.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.325
r_dihedral_angle_4_deg	18.12
r_dihedral_angle_3_deg	15.168
r_dihedral_angle_1_deg	7.164
r_angle_other_deg	2.368
r_angle_refined_deg	1.618
r_chiral_restr	0.074
r_bond_other_d	0.036
r_gen_planes_other	0.011
r_bond_refined_d	0.01
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5136
Nucleic Acid Atoms
Solvent Atoms	233
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
MOLREP	phasing