9GCJ | pdb_00009gcj

The crystal structure of beta-glucosidase from the thermophilic bacterium Caldicellulosiruptor saccharolyticus in complex with beta-D-glucose determined at 1.95 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9GCI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	292.15	Co-crystals: 0.2 M magnesium chloride hexahydrate, 0.1M Bis-Tris, pH 5.5, 25% (w/v) PEG 3350 in the presence of 0.6 mM lactose

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.161	α = 90
b = 98.307	β = 97.632
c = 81.776	γ = 90

Symmetry
Space Group	P 1 21 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 PILATUS 12M		2021-07-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9763	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.95	98.31	99.6	0.137	0.095	0.974	8.3	6.7		77506

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	1.99	99.9		1.655	0.634	0.653	1.8	6.7

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.95	62.615	77479	3968	99.508	0.173	0.1713	0.1746	0.2072	0.2106	31.517

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]
-1.368		-2.456	2.266		-0.231

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.538
r_dihedral_angle_3_deg	12.115
r_dihedral_angle_1_deg	6.339
r_lrange_it	6.115
r_lrange_other	6.091
r_dihedral_angle_2_deg	6.035
r_scangle_it	4.905
r_scangle_other	4.905
r_scbond_it	3.07
r_scbond_other	3.07
r_mcangle_it	2.819
r_mcangle_other	2.818
r_mcbond_it	1.916
r_mcbond_other	1.913
r_angle_refined_deg	1.197
r_angle_other_deg	0.408
r_nbd_other	0.258
r_nbd_refined	0.213
r_symmetry_nbd_refined	0.193
r_nbtor_refined	0.191
r_symmetry_nbd_other	0.187
r_xyhbond_nbd_refined	0.144
r_symmetry_xyhbond_nbd_refined	0.109
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.059
r_gen_planes_refined	0.006
r_bond_refined_d	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7588
Nucleic Acid Atoms
Solvent Atoms	402
Heterogen Atoms	64

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
BALBES	phasing