9QC9 | pdb_00009qc9

Yeast 20S proteasome double mutant: beta5_F(-46)S / beta5_G128V

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5CZ4	Yeast 20S proteasome at 2.3 A resolution

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
3.61	65.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 134.72	α = 90
b = 300.35	β = 112.8
c = 144.55	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	DECTRIS EIGER X 16M		2016-11-20	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	2.6	30	97.8	0.064	15.5	3.2		316457

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	2.6	2.7	98.1		0.501	3	3.1

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.6	15	299136	15744	97.38	0.18758	0.18563	0.1847	0.22441	0.2232	RANDOM	51.841

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]
-1.33		-1.23	4.55		-1.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.397
r_dihedral_angle_4_deg	16.34
r_dihedral_angle_3_deg	15.678
r_long_range_B_refined	6.674
r_long_range_B_other	6.518
r_dihedral_angle_1_deg	6.487
r_rigid_bond_restr	4.73
r_mcangle_it	4.151
r_mcangle_other	4.151
r_scangle_other	4.105
r_scbond_it	2.926
r_scbond_other	2.926
r_mcbond_it	2.898
r_mcbond_other	2.898
r_angle_refined_deg	1.242
r_angle_other_deg	1.139
r_chiral_restr	0.043
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.002
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
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	49473
Nucleic Acid Atoms
Solvent Atoms	835
Heterogen Atoms	120

Software

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