9IQB | pdb_00009iqb

Crystal structure of beta-glucosidase from Acetivibrio thermocellus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3AHX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	295	0.1M HEPES, 55% MPD

Crystal Properties
Matthews coefficient	Solvent content
3.86	68.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.93	α = 60.118
b = 158.62	β = 88.192
c = 158.91	γ = 87.478

Symmetry
Space Group	P 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	IMAGE PLATE	RIGAKU RAXIS IV++		2019-01-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54179

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	3	35	93.9	0.165	0.233	0.97	4.33	1.99		175099

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.2			0.65	0.92	0.5

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	3	34.991	175099	8755	94.062	0.335	0.3	0.3115	0.35	0.3206	39.256

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]
0.036	0.023	0.014	-0.008	0.008	-0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.756
r_dihedral_angle_4_deg	20.401
r_dihedral_angle_3_deg	16.489
r_dihedral_angle_1_deg	7.467
r_lrange_other	6.738
r_lrange_it	6.737
r_mcangle_it	3.631
r_mcangle_other	3.631
r_scangle_it	2.757
r_scangle_other	2.756
r_mcbond_it	2.154
r_mcbond_other	2.153
r_scbond_it	1.554
r_scbond_other	1.553
r_angle_refined_deg	1.407
r_angle_other_deg	1.142
r_nbd_other	0.3
r_symmetry_nbd_refined	0.241
r_nbd_refined	0.23
r_xyhbond_nbd_refined	0.23
r_symmetry_nbd_other	0.222
r_symmetry_xyhbond_nbd_refined	0.221
r_nbtor_refined	0.17
r_symmetry_xyhbond_nbd_other	0.085
r_xyhbond_nbd_other	0.079
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.053
r_bond_refined_d	0.005
r_bond_other_d	0.005
r_gen_planes_refined	0.005
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	43908
Nucleic Acid Atoms
Solvent Atoms	303
Heterogen Atoms	16

Software

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