3D6E

Crystal structure of the engineered 1,3-1,4-beta-glucanase protein from Bacillus licheniformis

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	16% PEG MME 2000, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.551	α = 61.38
b = 54.813	β = 85.72
c = 54.91	γ = 86.1

Symmetry
Space Group	P 1

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 QUANTUM 315	mirrors	2008-02-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.9795	ESRF	ID23-1

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	2.4	30	93.5	0.043	0.037	18.7	1.8	14740	14739	1	1	15

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)
	2.4	2.49	79.2		0.121	0.126	6.25	1.6	14739

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	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	PDB ENTRY 1GBG	2.4	30	1	1	14740	14011	731	93.43	0.21259	0.21042	0.25481	RANDOM	19.538

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]
-1.17	-0.24	-0.16	0.48	0.39	0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.258
r_dihedral_angle_4_deg	15.648
r_dihedral_angle_3_deg	11.135
r_dihedral_angle_1_deg	6.291
r_angle_refined_deg	1.093
r_angle_other_deg	1.055
r_scangle_it	0.508
r_mcangle_it	0.436
r_scbond_it	0.325
r_mcbond_it	0.244
r_chiral_restr	0.182
r_nbtor_refined	0.18
r_nbd_other	0.177
r_nbd_refined	0.148
r_xyhbond_nbd_refined	0.133
r_symmetry_vdw_refined	0.133
r_symmetry_vdw_other	0.12
r_nbtor_other	0.079
r_metal_ion_refined	0.072
r_xyhbond_nbd_other	0.033
r_symmetry_hbond_refined	0.031
r_mcbond_other	0.023
r_bond_refined_d	0.005
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2953
Nucleic Acid Atoms
Solvent Atoms	137
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
DNA	data collection
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing