1V0M

Xylanase Xyn10a from Streptomyces lividans in complex with xylobio-deoxynojirimycin at pH 7.5

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OD8	PDB ENTRY 1OD8

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2	36.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.884	α = 90
b = 46.081	β = 90
c = 85.789	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	SAGITALLY FOCUSING GE(220) AND A MULTILAYER	2002-09-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1		ESRF	ID14-1

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	1.07	20	94.4	0.063	25.54	5.7		117436

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	1.07	1.11	81.2		0.466	2.94	5.93

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 1OD8	1.07	19.65	105254	5530	94.4	0.099	0.098	0.121	RANDOM	7.7

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]
0.92			-0.95		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.261
r_dihedral_angle_4_deg	14.688
r_dihedral_angle_3_deg	10.979
r_dihedral_angle_1_deg	6.293
r_scangle_it	3.377
r_scbond_it	2.672
r_mcangle_it	1.995
r_mcbond_it	1.653
r_angle_refined_deg	1.652
r_angle_other_deg	1.1
r_mcbond_other	0.644
r_symmetry_vdw_other	0.31
r_nbd_refined	0.231
r_nbd_other	0.22
r_symmetry_hbond_refined	0.215
r_xyhbond_nbd_refined	0.16
r_chiral_restr	0.122
r_symmetry_vdw_refined	0.113
r_nbtor_other	0.095
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_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	2330
Nucleic Acid Atoms
Solvent Atoms	568
Heterogen Atoms	23

Software

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