8KAP | pdb_00008kap

Glycoside hydrolase family 1 beta-glucosidase from Streptomyces griseus (ligand-free)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4R27

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.1 M Bis-Tris (pH 5.5), 0.2 M ammonium acetate, 15% (w/v) PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.858	α = 90
b = 97.756	β = 90
c = 184.874	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 PILATUS3 S 2M		2020-11-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1	Photon Factory	AR-NW12A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.2	48.43	100	0.991	8.8	6.6		89749

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.24	100		0.685

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.2	46.261	89668	4438	99.936	0.233	0.232	0.24	0.2568	0.26	25.474

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]
-0.448			-2.656		3.105

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.719
r_dihedral_angle_6_deg	13.108
r_dihedral_angle_1_deg	6.464
r_dihedral_angle_2_deg	4.976
r_lrange_it	1.562
r_lrange_other	1.562
r_angle_refined_deg	0.863
r_mcangle_it	0.772
r_mcangle_other	0.772
r_angle_other_deg	0.54
r_scangle_it	0.483
r_scangle_other	0.483
r_mcbond_it	0.41
r_mcbond_other	0.41
r_scbond_it	0.24
r_scbond_other	0.24
r_symmetry_nbd_other	0.209
r_nbd_refined	0.185
r_nbtor_refined	0.176
r_nbd_other	0.175
r_xyhbond_nbd_refined	0.109
r_symmetry_xyhbond_nbd_refined	0.104
r_symmetry_nbd_refined	0.102
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.047
r_symmetry_xyhbond_nbd_other	0.033
r_gen_planes_refined	0.003
r_gen_planes_other	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12240
Nucleic Acid Atoms
Solvent Atoms	302
Heterogen Atoms	113

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
MOLREP	phasing
ARP/wARP	model building
Aimless	data scaling