4UZN | pdb_00004uzn

The native structure of the family 46 carbohydrate-binding module (CBM46) of endo-beta-1,4-glucanase B (Cel5B) from Bacillus halodurans

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4UZ8	PDB ENTRY 4UZ8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		0.4-0.75 M POTASSIUM SODIUM TARTRATE TETRAHYDRATE PROTEIN WAS COCRYSTALLISED WITH 10 MM OF 1,4-BETA-D-CELLOHEXAOSEIN 50 MM HEPES HCL PH 7.5, 200 MM NACL, 5 MM CACL2. 30%, V/V GLYCEROL ADDED TO THE CRYSTALLIZATION BUFFER AS CRYOPROTECTANT.

Crystal Properties
Matthews coefficient	Solvent content
2.5	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.19	α = 90
b = 121.19	β = 90
c = 77.28	γ = 90

Symmetry
Space Group	I 41 2 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	PIXEL	DECTRIS PILATUS 6M		2012-09-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1		Diamond	I04-1

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	2.46	44.37	99.8	0.13	9.7	8.2		10730

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	2.46	2.56	100		1.5	1.3	7.7

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 4UZ8	2.46	85.69	10178	519	99.43	0.21558	0.21429	0.22	0.23997	0.24	RANDOM	68.816

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]
-4.99			-4.99		9.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.285
r_dihedral_angle_4_deg	17.132
r_dihedral_angle_3_deg	15.114
r_dihedral_angle_1_deg	7.217
r_mcangle_it	2.156
r_scbond_it	1.42
r_angle_refined_deg	1.407
r_mcbond_it	1.321
r_mcbond_other	1.32
r_angle_other_deg	0.844
r_chiral_restr	0.072
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
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	1632
Nucleic Acid Atoms
Solvent Atoms	23
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
FAST_DP	data scaling
PHASER	phasing