5L5F | pdb_00005l5f

Yeast 20S proteasome with human beta5i (1-138) and human beta6 (97-111; 118-133) in complex with bortezomib

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 = 135.51	α = 90
b = 300.91	β = 112.59
c = 144.92	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		2015-07-11	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	2.5	30	98.2	0.068	11.5	3.3		361627

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	2.5	2.6	98.3		0.469	2.3

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5CZ4	2.5	15	343544	18082	98.29	0.20623	0.20507	0.21	0.22808	0.23	RANDOM	58.254

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]
2.42		-0.57	-3.65		1.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.217
r_sphericity_free	30.212
r_dihedral_angle_3_deg	14.253
r_dihedral_angle_4_deg	14.002
r_sphericity_bonded	13.202
r_dihedral_angle_1_deg	4.963
r_long_range_B_refined	2.989
r_long_range_B_other	2.949
r_mcangle_it	2.496
r_mcangle_other	2.496
r_scangle_other	2.167
r_mcbond_it	1.892
r_mcbond_other	1.892
r_scbond_it	1.82
r_scbond_other	1.82
r_rigid_bond_restr	1.478
r_angle_refined_deg	0.893
r_angle_other_deg	0.735
r_chiral_restr	0.049
r_bond_refined_d	0.004
r_gen_planes_refined	0.003
r_bond_other_d	0.002
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	49382
Nucleic Acid Atoms
Solvent Atoms	884
Heterogen Atoms	180

Software

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