7VOH | pdb_00007voh

The a-glucosidase QsGH13 from Qipengyuania seohaensis

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	277	0.1 M Tris, pH 8.5, 0.2 MNaCl, 25% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.815	α = 90
b = 129.918	β = 90
c = 161.304	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 315		2015-10-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.9793	SSRF	BL17U

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.197	50	99.4	0.115	0.993	14.36	6.95		63387

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.33	97.7		0.246	0.932		6.14

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	6AAV	2.197	34.28	63387	3245	99.54	0.221	0.2183	0.22	0.2738	0.28	22.332

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]
-0.54			1.013		-0.473

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.24
r_dihedral_angle_4_deg	17.811
r_dihedral_angle_3_deg	14.672
r_dihedral_angle_1_deg	7.507
r_lrange_it	4.599
r_lrange_other	4.403
r_mcangle_it	2.414
r_mcangle_other	2.414
r_scangle_it	2.111
r_scangle_other	2.11
r_mcbond_it	1.528
r_mcbond_other	1.528
r_angle_other_deg	1.38
r_angle_refined_deg	1.377
r_scbond_it	1.338
r_scbond_other	1.338
r_xyhbond_nbd_refined	0.243
r_nbd_refined	0.203
r_symmetry_nbd_other	0.199
r_nbtor_refined	0.173
r_symmetry_xyhbond_nbd_refined	0.149
r_symmetry_nbd_refined	0.136
r_nbd_other	0.125
r_symmetry_xyhbond_nbd_other	0.088
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.07
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8222
Nucleic Acid Atoms
Solvent Atoms	770
Heterogen Atoms	16

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing