6ZPV | pdb_00006zpv

Structure of Unliganded MgGH51 a-L-Arabinofuranosidase Crystal Type 3

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		293	10 mg/mL MgGH51 in 10 mM NaOAc pH 5.5, 100 mM NaCl mixed 2:1 with 1.8 M (NH4)2SO4, 0.1 M NaOAc, pH 5-6, 35% glycerol

Crystal Properties
Matthews coefficient	Solvent content
3.34	63.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.953	α = 90
b = 83.953	β = 90
c = 256.589	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	PIXEL	DECTRIS PILATUS 2M		2019-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I23	1.3775	Diamond	I23

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	1.2	85.53	100	0.011	1	27.2	33		285059

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	1.2	1.22	100		0.43	0.421	1.8	25.1

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 (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	1.2	79.918	284861	14149	99.971	0.121	0.1199	0.12	0.144	0.14	15.41

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]
0.167			0.167		-0.334

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.969
r_dihedral_angle_4_deg	14.656
r_dihedral_angle_3_deg	11.45
r_rigid_bond_restr	7.532
r_dihedral_angle_1_deg	7.057
r_scbond_it	4.656
r_scbond_other	4.655
r_scangle_it	4.425
r_scangle_other	4.425
r_lrange_it	3.806
r_lrange_other	3.681
r_angle_refined_deg	2.073
r_angle_other_deg	1.647
r_mcangle_it	1.327
r_mcangle_other	1.327
r_mcbond_it	1.159
r_mcbond_other	1.153
r_symmetry_xyhbond_nbd_other	0.319
r_nbd_other	0.236
r_nbd_refined	0.233
r_xyhbond_nbd_refined	0.23
r_symmetry_nbd_other	0.19
r_symmetry_xyhbond_nbd_refined	0.185
r_nbtor_refined	0.181
r_symmetry_nbd_refined	0.174
r_chiral_restr	0.13
r_symmetry_nbtor_other	0.09
r_xyhbond_nbd_other	0.035
r_bond_refined_d	0.018
r_gen_planes_refined	0.013
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4788
Nucleic Acid Atoms
Solvent Atoms	1082
Heterogen Atoms	264

Software

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