1YI7 | pdb_00001yi7

Beta-d-xylosidase (selenomethionine) XYND from Clostridium Acetobutylicum

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Y7B	PDB entry 1Y7B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	295	0.1 M HEPES, 0.2 M AMMONIUM SULFATE, 15% PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.13	α = 90
b = 143.73	β = 90
c = 188.69	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	105	IMAGE PLATE	RIGAKU RAXIS IV	VARIMAX	2004-12-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

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	1.9	40	100	0.11	10.8	7.8	190582	190582		-5	17.8

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	1.9	1.97	100		0.38	4.8	7.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 1Y7B	1.9	20	184667	184667	5740	100	0.144	0.144	0.142	0.1489	0.202	0.2093	RANDOM	24.975

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]
0.4			-0.02		-0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.893
r_dihedral_angle_4_deg	19.428
r_scangle_it	13.932
r_scbond_it	13.324
r_dihedral_angle_3_deg	13.265
r_mcangle_it	7.155
r_dihedral_angle_1_deg	6.745
r_mcbond_it	6.061
r_angle_refined_deg	1.379
r_nbtor_refined	0.323
r_symmetry_vdw_refined	0.26
r_nbd_refined	0.206
r_symmetry_hbond_refined	0.155
r_xyhbond_nbd_refined	0.132
r_metal_ion_refined	0.121
r_chiral_restr	0.104
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17364
Nucleic Acid Atoms
Solvent Atoms	2586
Heterogen Atoms	219

Software

Software
Software Name	Purpose
REFMAC	refinement
AMoRE	phasing