1OIM | pdb_00001oim

Family 1 b-glucosidase from Thermotoga maritima

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OD0	PDB ENTRY 1OD0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		10MG/ML PROTEIN IN 15% PEG 4K, 0.2 M CAAC, 0.1M IMIDAZOLE PH7, pH 7.00

Crystal Properties
Matthews coefficient	Solvent content
2.3	46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.688	α = 90
b = 94.473	β = 90
c = 113.824	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 CCD		2001-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.15	20	99.5	0.051	24.82	3.73		207372

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.23	98.9		0.373	3.85	3.39

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 (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	PDB ENTRY 1OD0	2.15	72.55	52990	2831	99.3	0.191	0.189	0.19	0.233	0.23	RANDOM	36.2

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]
-1.02			0.24		0.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.261
r_scangle_it	3.448
r_scbond_it	2.232
r_mcangle_it	1.377
r_angle_refined_deg	1.372
r_mcbond_it	0.723
r_nbd_refined	0.204
r_symmetry_vdw_refined	0.191
r_symmetry_hbond_refined	0.143
r_xyhbond_nbd_refined	0.142
r_chiral_restr	0.096
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7120
Nucleic Acid Atoms
Solvent Atoms	493
Heterogen Atoms	22

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling