6ZPY | pdb_00006zpy

Structure of Arabinose-Bound MgGH51 a-L-Arabinofuranosidase Crystal Type 1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6ZPS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	10 mg/mL MgGH51 in 10 mM NaOAc, pH 5.5, 100 mM NaCl mixed 2:1 with 20% PEG 3350, 0.1 M Bis-Tris-HCl, pH 6.5, 0.2 M NaNO3

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.708	α = 90
b = 65.043	β = 90
c = 174.122	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	PIXEL	DECTRIS PILATUS 6M-F		2019-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9119	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.27	65.04	98.5	0.04	0.996	8.7	7.9		176357			11.14

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.27	1.29	97.3		0.374	0.764	0.8	7.3

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	6ZPS	1.27	56.544	176207	8652	98.391	0.141	0.1394	0.15	0.1788	0.19	14.949

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]
-0.47			0.705		-0.235

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.103
r_dihedral_angle_4_deg	16.086
r_dihedral_angle_3_deg	11.616
r_dihedral_angle_1_deg	7.192
r_rigid_bond_restr	3.024
r_lrange_it	2.801
r_scangle_it	2.568
r_scangle_other	2.551
r_lrange_other	2.517
r_scbond_it	2.226
r_scbond_other	2.214
r_angle_refined_deg	1.833
r_mcangle_it	1.745
r_mcangle_other	1.745
r_angle_other_deg	1.641
r_mcbond_it	1.5
r_mcbond_other	1.5
r_nbd_refined	0.207
r_nbtor_refined	0.187
r_symmetry_nbd_other	0.184
r_symmetry_xyhbond_nbd_refined	0.146
r_xyhbond_nbd_refined	0.136
r_nbd_other	0.135
r_chiral_restr	0.105
r_symmetry_nbtor_other	0.089
r_symmetry_nbd_refined	0.033
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4775
Nucleic Acid Atoms
Solvent Atoms	818
Heterogen Atoms	150

Software

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