4R18

Ligand-induced Lys33-Thr1 crosslinking 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	VAPOR DIFFUSION, HANGING DROP	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 = 136.58	α = 90
b = 300.82	β = 113.2
c = 146.29	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		2013-05-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0	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	2.4	30	96.9	0.044	17.3	3.1		408278	2	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	2.4	2.5	97.8		0.417	4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1RYP	2.4	15	408277	387863	20414	96.99	0.181	0.17806	0.17718	0.19486	RANDOM	56.74

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]
3.41		-0.67	-4.79		1.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.121
r_sphericity_free	25.257
r_dihedral_angle_3_deg	17.178
r_dihedral_angle_4_deg	17.176
r_sphericity_bonded	8.08
r_dihedral_angle_1_deg	5.801
r_long_range_B_refined	2.617
r_long_range_B_other	2.504
r_scangle_other	1.956
r_scbond_it	1.93
r_scbond_other	1.929
r_mcangle_it	1.848
r_mcangle_other	1.848
r_mcbond_it	1.576
r_mcbond_other	1.576
r_rigid_bond_restr	1.47
r_angle_refined_deg	0.976
r_angle_other_deg	0.706
r_chiral_restr	0.056
r_bond_refined_d	0.004
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	49352
Nucleic Acid Atoms
Solvent Atoms	1740
Heterogen Atoms	23

Software

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