5JHR

Yeast 20S proteasome in complex with the peptidic epoxyketone inhibitor 27

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5CZ4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	293	20 mM MgAC2, 13% MPD, 0.1 M MES

Crystal Properties
Matthews coefficient	Solvent content
3.67	66.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.29	α = 90
b = 300.81	β = 112.95
c = 144.54	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		2014-09-07	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	2.9	50	97.7	0.074	12.9	3.1		229229

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	2.9	3	99.1		0.523	2.7

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	5CZ4	2.9	15	217766	11462	97.84	0.18226	0.18101	0.20615	RANDOM	67.841

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]
2.4		-1.39	-6.37		3.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.919
r_sphericity_free	33.59
r_dihedral_angle_4_deg	15.323
r_dihedral_angle_3_deg	15.315
r_sphericity_bonded	5.707
r_dihedral_angle_1_deg	4.973
r_long_range_B_refined	3.132
r_long_range_B_other	3.111
r_mcangle_it	2.744
r_mcangle_other	2.744
r_scangle_other	2.482
r_mcbond_it	2.082
r_mcbond_other	2.082
r_scbond_it	2.041
r_scbond_other	2.041
r_rigid_bond_restr	1.646
r_angle_refined_deg	0.92
r_angle_other_deg	0.694
r_chiral_restr	0.051
r_bond_refined_d	0.004
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	49304
Nucleic Acid Atoms
Solvent Atoms	216
Heterogen Atoms	135

Software

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