5A8O

Crystal structure of beta-glucanase SdGluc5_26A from Saccharophagus degradans in complex with cellotetraose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5A8N	PDB ENTRY 5A8N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6		0.2 M AMMONIUM SULPHATE, 0.1 M SODIUM CACODYLATE BUFFER PH 6.0, 25% (W/V) PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
3.11	60.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.773	α = 90
b = 143.773	β = 90
c = 143.773	γ = 90

Symmetry
Space Group	P 41 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100		DECTRIS P		2013-05-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1		SOLEIL	PROXIMA 1

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	2.3	47.92	100	0.11	17.5	9.5		23212			23.16

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	2.3	2.42	100		0.58	4	9.5

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 5A8N	2.3	45.51	21999	1171	99.88	0.15067	0.14946	0.17282	RANDOM	26.595

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.268
r_dihedral_angle_4_deg	14.347
r_dihedral_angle_3_deg	12.52
r_dihedral_angle_1_deg	5.814
r_angle_refined_deg	1.191
r_angle_other_deg	0.749
r_symmetry_vdw_refined	0.269
r_nbd_refined	0.238
r_symmetry_hbond_refined	0.238
r_nbtor_refined	0.188
r_xyhbond_nbd_other	0.176
r_nbd_other	0.17
r_symmetry_vdw_other	0.15
r_xyhbond_nbd_refined	0.128
r_nbtor_other	0.081
r_chiral_restr	0.069
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2775
Nucleic Acid Atoms
Solvent Atoms	291
Heterogen Atoms	99

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing