3GNP

Crystal Structure of a Rice Os3BGlu6 Beta-Glucosidase with Octyl-Beta-D-Thio-Glucoside

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	288	19% PEG5000 MME, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.185	α = 90
b = 91.093	β = 90
c = 111.359	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	110	CCD	ADSC QUANTUM 315		2009-01-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13B1	1.0000	NSRRC	BL13B1

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	1.8	30	91.1	0.052	30.7	6.9	49796	48102			18.1

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	1.8	1.86	98		0.293	6.4	6.9	5274

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3GNO	1.8	26.82	51743	47066	2540	90.96	0.17994	0.17847	0.2066	RANDOM	19.485

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]
0.01			-0.01		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.943
r_dihedral_angle_4_deg	18.808
r_dihedral_angle_3_deg	13.22
r_dihedral_angle_1_deg	13.14
r_scangle_it	3.443
r_scbond_it	2.253
r_angle_refined_deg	1.443
r_mcangle_it	1.402
r_mcbond_it	0.791
r_nbtor_refined	0.313
r_nbd_refined	0.206
r_symmetry_vdw_refined	0.189
r_xyhbond_nbd_refined	0.126
r_chiral_restr	0.1
r_symmetry_hbond_refined	0.063
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3842
Nucleic Acid Atoms
Solvent Atoms	340
Heterogen Atoms	44

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling