1OD8 | pdb_00001od8

Xylanase Xyn10A from Streptomyces lividans in complex with xylobio-isofagomine lactam

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1E0X	PDB ENTRY 1E0X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		20 MG/ML PROTEIN, 16% PEG 5K MME, 100 MM IMIDAZOLE, PH 7.5, 5% ISOPROPANOL

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.814	α = 90
b = 45.878	β = 90
c = 85.737	γ = 90

Symmetry
Space Group	P 21 21 21

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 CCD	TORROIDAL MIRROR	2002-09-15	M	SINGLE WAVELENGTH

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

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	1.05	20	98	0.062	26.4	4.7		121638

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	1.05	1.09	86.4		0.441	2.3	2.05

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 1E0X	1.05	19.8	112969	5945	97.9	0.104	0.103	0.12	0.126	0.14	RANDOM	8.12

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]
0.11			0.04		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.229
r_scangle_it	4.558
r_scbond_it	3.441
r_mcangle_it	2.81
r_mcbond_it	2.03
r_angle_refined_deg	1.689
r_angle_other_deg	0.85
r_metal_ion_refined	0.614
r_nbd_other	0.455
r_symmetry_vdw_other	0.427
r_symmetry_vdw_refined	0.382
r_metal_ion_other	0.335
r_nbd_refined	0.318
r_nbtor_other	0.298
r_chiral_restr	0.126
r_bond_refined_d	0.015
r_gen_planes_refined	0.004
r_bond_other_d
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbtor_refined
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
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	2324
Nucleic Acid Atoms
Solvent Atoms	629
Heterogen Atoms	50

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling