4XUP | pdb_00004xup

Structure of the N-terminal CBM22-1-CBM22-2 tandem domain from Paenibacillus barcinonensis Xyn10C

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DYO	1DYO and 2w5f
experimental model	PDB	2W5F	1DYO and 2w5f

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	291	23% PEG 3350, 0.2 M Calcium chloride, 0.1 M Bis Tris propane pH 5.5 Additive: 2% 1,6-Hexanediol Ratio (protein/precipitant/additive): 0.5/2/0.3 with streak seeding starting from spherulites.

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.17	α = 90
b = 110.359	β = 90.63
c = 118.522	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-F		2013-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.979235	ESRF	ID29

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	2.43	118.52	99.4	0.13	0.085	8.6	6.3		81116	1	1	37.24

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	2.43	2.48	99.3		0.8	2.2	6.5	5568

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	1DYO and 2w5f	2.43	118.52	77022	4072	99.28	0.22879	0.22687	0.23	0.26495	0.27	RANDOM	48.706

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]
0.12		-1.17	-2.43		2.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.587
r_dihedral_angle_4_deg	18.023
r_dihedral_angle_3_deg	14.507
r_long_range_B_refined	8.415
r_long_range_B_other	8.415
r_scangle_other	6.359
r_dihedral_angle_1_deg	5.985
r_mcangle_it	5.407
r_mcangle_other	5.407
r_scbond_it	4.104
r_scbond_other	4.103
r_mcbond_it	3.564
r_mcbond_other	3.563
r_angle_other_deg	1.967
r_angle_refined_deg	1.535
r_chiral_restr	0.079
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d	0.008
r_gen_planes_other	0.007
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12488
Nucleic Acid Atoms
Solvent Atoms	30
Heterogen Atoms	22

Software

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