4JIE

Structural analysis and insights into glycon specificity of the rice GH1 Os7BGlu26 beta-D-mannosidase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2RGL

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.01	α = 90
b = 73.624	β = 90
c = 133.984	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		2012-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13B1		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	2.25	27.82	77.53				29353		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	2.25	2.33	70.4

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	Rigid Body Refinement	THROUGHOUT	2RGL	2.45	26.22	20741	1113	86.35	0.15546	0.15328	0.1954	RANDOM	23.975

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]
-0.03			0.09		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.676
r_dihedral_angle_4_deg	17.845
r_dihedral_angle_3_deg	15.388
r_dihedral_angle_1_deg	5.922
r_scangle_it	2.133
r_scbond_it	1.299
r_angle_refined_deg	1.212
r_mcangle_it	0.933
r_mcbond_it	0.524
r_nbtor_refined	0.312
r_nbd_refined	0.196
r_symmetry_vdw_refined	0.161
r_xyhbond_nbd_refined	0.127
r_symmetry_hbond_refined	0.102
r_chiral_restr	0.09
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
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	3939
Nucleic Acid Atoms
Solvent Atoms	231
Heterogen Atoms	63

Software

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