6ZPZ | pdb_00006zpz

Structure of a-l-AraCS-Bound MgGH51 a-L-Arabinofuranosidase Crystal Type 1

X-RAY DIFFRACTION

---

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
2.7	54.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 191.63	α = 90
b = 58.09	β = 90
c = 65.71	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	1.71	58.12	98.8	0.052	0.997	8.7	7.5		79871			21.04

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	1.71	1.74	98.5		0.694	0.419		6.7

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	1.71	55.654	79795	3991	99.413	0.189	0.1867	0.19	0.2245	0.23	23.46

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]
-0.989			1.04		-0.051

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.363
r_dihedral_angle_4_deg	13.683
r_dihedral_angle_3_deg	12.084
r_dihedral_angle_1_deg	7.601
r_lrange_it	4.033
r_lrange_other	3.981
r_scangle_it	3.17
r_scangle_other	3.17
r_scbond_it	2.258
r_scbond_other	2.255
r_mcangle_it	2.208
r_mcangle_other	2.208
r_angle_refined_deg	1.746
r_mcbond_it	1.736
r_mcbond_other	1.735
r_angle_other_deg	1.506
r_symmetry_xyhbond_nbd_refined	0.321
r_nbd_refined	0.207
r_symmetry_nbd_other	0.197
r_nbd_other	0.187
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.146
r_symmetry_nbd_refined	0.088
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.078
r_symmetry_xyhbond_nbd_other	0.07
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4763
Nucleic Acid Atoms
Solvent Atoms	567
Heterogen Atoms	138

Software

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