5A95 | pdb_00005a95

Crystal structure of beta-glucanase SdGluc5_26A from Saccharophagus degradans in complex with tetrasaccharide A, form 2

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		7.5		30% (W/V) PEG 4000, 0.1 M TRIS BUFFER PH 7.5, 0.2 M MGCL2

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.048	α = 90
b = 60.384	β = 104.75
c = 130.326	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS PILATUS 6M		2013-09-11	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	1.35	45.63	100	0.06	10.5	3.7		237302			11.06

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	1.35	1.42	99.9		0.44	2.6	3.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 5A8N	1.35	45.44	225378	11901	99.98	0.13071	0.12938	0.13	0.1561	0.16	RANDOM	13.522

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]
0.2		0.14	-0.01		-0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.209
r_sphericity_free	31.427
r_dihedral_angle_4_deg	13.915
r_dihedral_angle_3_deg	10.999
r_rigid_bond_restr	8.621
r_sphericity_bonded	7.929
r_dihedral_angle_1_deg	6.297
r_angle_refined_deg	1.427
r_angle_other_deg	0.918
r_symmetry_vdw_refined	0.316
r_nbd_refined	0.27
r_nbtor_refined	0.191
r_nbd_other	0.18
r_xyhbond_nbd_refined	0.158
r_symmetry_vdw_other	0.154
r_symmetry_hbond_refined	0.111
r_chiral_restr	0.093
r_nbtor_other	0.082
r_xyhbond_nbd_other	0.054
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8326
Nucleic Acid Atoms
Solvent Atoms	1740
Heterogen Atoms	128

Software

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