4YA1

Yeast 20S proteasome beta2-H116N mutant

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, 0.1 M MES

Crystal Properties
Matthews coefficient	Solvent content
3.67	66.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 134.86	α = 90
b = 302.06	β = 112.8
c = 144.23	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		2014-04-12	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 Sym 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	92.2	0.105	9	2.9	216178	216178

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	95.1		0.521	3

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	1RYP	2.9	15	205369	10809	92.3	0.1988	0.19781	0.21779	RANDOM	54.189

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]
2.72		-1.96	-5.32		2.52

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	36.103
r_dihedral_angle_2_deg	34.547
r_dihedral_angle_4_deg	14.772
r_dihedral_angle_3_deg	14.691
r_dihedral_angle_1_deg	5.217
r_sphericity_bonded	4.103
r_long_range_B_refined	2.288
r_long_range_B_other	2.265
r_mcangle_it	1.822
r_mcangle_other	1.822
r_scangle_other	1.747
r_scbond_it	1.547
r_scbond_other	1.547
r_mcbond_it	1.433
r_mcbond_other	1.433
r_rigid_bond_restr	1.276
r_angle_refined_deg	0.871
r_angle_other_deg	0.682
r_chiral_restr	0.051
r_bond_refined_d	0.004
r_gen_planes_refined	0.002
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	49372
Nucleic Acid Atoms
Solvent Atoms	348
Heterogen Atoms	13

Software

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