4R17

Ligand-induced aziridine-formation at subunit beta5 of the yeast 20S proteasome

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.8	293	20 MM MGAC2, 13% MPD, PH 6.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

Crystal Properties
Matthews coefficient	Solvent content
3.67	66.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 134.72	α = 90
b = 301.36	β = 112.81
c = 144.74	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	PSI PILATUS 6M		2013-06-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA		SLS	X06SA

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	2.1	30	98.8	0.044	18.3	3.1		608720		2

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	2.1	2.2	99.4		0.568	2.9

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1RYP	2.1	15	608720	578284	30436	98.9	0.186	0.185	0.198	RANDOM	46.42

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]
1.89		-0.5	-3.72		1.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.265
r_sphericity_free	23.417
r_dihedral_angle_4_deg	18.338
r_dihedral_angle_3_deg	17.436
r_dihedral_angle_1_deg	6.174
r_sphericity_bonded	4.251
r_long_range_B_refined	2.366
r_long_range_B_other	2.056
r_rigid_bond_restr	1.892
r_scbond_it	1.771
r_scbond_other	1.771
r_scangle_other	1.514
r_mcangle_it	1.289
r_mcangle_other	1.289
r_mcbond_it	1.238
r_mcbond_other	1.238
r_angle_refined_deg	1.095
r_angle_other_deg	0.744
r_chiral_restr	0.096
r_bond_refined_d	0.005
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	49336
Nucleic Acid Atoms
Solvent Atoms	3472
Heterogen Atoms	23

Software

Software
Software Name	Purpose
XDS	data scaling
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing