9VSF | pdb_00009vsf

GH64 Beta-1,3-glucanase from Candidatus Saccharibacteria bacterium

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	7.5	298	0.1M HEPES, 0.8M Potassium sodium tartrate

Crystal Properties
Matthews coefficient	Solvent content
3.05	59.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.63	α = 90
b = 100.59	β = 90.69
c = 113.168	γ = 90

Symmetry
Space Group	I 1 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 EIGER2 S 9M		2024-12-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL02U1	0.979145	SSRF	BL02U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.13	56.31	99.8	0.161	0.174	0.067	0.996	9.8	6.8		70371

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.13	2.18	100		1.108	1.196	0.447	0.774	2.1	7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.13	56.31	66968	3389	99.71	0.20433	0.20148	0.209	0.25907	0.2621	RANDOM	33.105

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]
-1.32		0.27	-3.49		4.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.958
r_dihedral_angle_2_deg	10.284
r_dihedral_angle_1_deg	7.806
r_long_range_B_other	6.487
r_long_range_B_refined	6.47
r_scangle_other	5.094
r_mcangle_it	4.374
r_mcangle_other	4.374
r_scbond_it	3.34
r_scbond_other	3.339
r_mcbond_it	3.02
r_mcbond_other	3.02
r_angle_refined_deg	1.806
r_angle_other_deg	0.623
r_chiral_restr	0.088
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7153
Nucleic Acid Atoms
Solvent Atoms	370
Heterogen Atoms	1

Software

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