3GD9

Crystal structure of laminaripentaose-producing beta-1,3-glucanase in complex with laminaritetraose

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIQUID DIFFUSION	6.5	293	0.05M ammonium sulfate, 20% PEG8000, 0.1M sodium cacodylate (pH6.5), 20mM laminaripentaose, LIQUID DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.981	α = 90
b = 60.352	β = 90
c = 149.118	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	77	CCD	ADSC QUANTUM 315		2006-08-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13B1	0.9795	NSRRC	BL13B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	97	0.04	0.038	41.7	8.3	39457	38270	325.5	103.9	18.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.8	1.86	89.2		0.117	0.104	19.5	8.2	3462

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	PDB ENTRY 3GD0	1.8	30	36280	1919	97.02	0.172	0.166	0.217	RANDOM	18.709

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]
-0.37			-0.61		0.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.586
r_dihedral_angle_4_deg	20.845
r_dihedral_angle_3_deg	15.311
r_dihedral_angle_1_deg	6.856
r_scangle_it	2.971
r_mcangle_it	2.473
r_scbond_it	2.004
r_mcbond_it	1.597
r_angle_refined_deg	1.185
r_nbtor_refined	0.323
r_symmetry_vdw_refined	0.244
r_nbd_refined	0.222
r_xyhbond_nbd_refined	0.182
r_symmetry_hbond_refined	0.177
r_chiral_restr	0.104
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
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	2757
Nucleic Acid Atoms
Solvent Atoms	652
Heterogen Atoms	45

Software

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