4RE3

Different transition state conformations for the hydrolysis of beta-mannosides and beta-glucosides in the rice Os7BGlu26 family GH1 beta-mannosidase/beta-glucosidase

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.25	288	0.8M K/Na tartrate, 0.1 M HEPES, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 288K

Crystal Properties
Matthews coefficient	Solvent content
2.97	58.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.1	α = 90
b = 73.209	β = 90
c = 134.047	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		2009-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13B1	1.00	NSRRC	BL13B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.55	30	99.9			22658	22658		1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.55	2.64	100

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4JHO	2.55	24.95	21454	1153	99.9	0.17725	0.17527	0.21316	RANDOM	20.804

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]
-0.41			1.87		-1.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.985
r_dihedral_angle_4_deg	17.438
r_dihedral_angle_3_deg	15.648
r_dihedral_angle_1_deg	5.986
r_scangle_it	2.704
r_scbond_it	1.892
r_angle_refined_deg	1.288
r_mcangle_it	1.095
r_mcbond_it	0.885
r_nbtor_refined	0.314

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.985
r_dihedral_angle_4_deg	17.438
r_dihedral_angle_3_deg	15.648
r_dihedral_angle_1_deg	5.986
r_scangle_it	2.704
r_scbond_it	1.892
r_angle_refined_deg	1.288
r_mcangle_it	1.095
r_mcbond_it	0.885
r_nbtor_refined	0.314
r_nbd_refined	0.204
r_symmetry_hbond_refined	0.161
r_symmetry_vdw_refined	0.148
r_xyhbond_nbd_refined	0.129
r_chiral_restr	0.097
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3934
Nucleic Acid Atoms
Solvent Atoms	119
Heterogen Atoms	61

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.