4HRC

Crystal structure of yeast 20S proteasome in complex with epoxyketone carmaphycin analogue 3

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	297	30 mM of magnesium acetate, 100 mM of MES (pH 7.2) and 12% of MPD, vapor diffusion, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
3.85	68.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.35	α = 90
b = 300.88	β = 112.74
c = 144.25	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		2012-06-02	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	2.7	48	97.8	0.078	9.33			284264		-3	63.57

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	2.7	2.8	97.5		0.541	1.76

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.8	48	255047	12670	98.01	0.2119	0.2102	0.2434	RANDOM	75.556

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]
3.27		-3.44	-9.28		3.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.582
r_dihedral_angle_3_deg	16.474
r_dihedral_angle_4_deg	14.575
r_dihedral_angle_1_deg	5.191
r_angle_refined_deg	0.999
r_scangle_it	0.825
r_scbond_it	0.462
r_mcangle_it	0.339
r_mcbond_it	0.177
r_chiral_restr	0.065

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.582
r_dihedral_angle_3_deg	16.474
r_dihedral_angle_4_deg	14.575
r_dihedral_angle_1_deg	5.191
r_angle_refined_deg	0.999
r_scangle_it	0.825
r_scbond_it	0.462
r_mcangle_it	0.339
r_mcbond_it	0.177
r_chiral_restr	0.065
r_bond_refined_d	0.006
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	49522
Nucleic Acid Atoms
Solvent Atoms	415
Heterogen Atoms	222

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.