5LF7 | pdb_00005lf7

Human 20S proteasome complex with Ixazomib at 2.0 Angstrom

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5LE5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	0.1 M Bis-Tris, 0.2 M Magnesium Chloride, 10 % PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.41	α = 90
b = 202.61	β = 90
c = 314.51	γ = 90

Symmetry
Space Group	P 21 21 21

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 PILATUS 6M-F	CRL Transfocator	2015-08-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.9763	PETRA III, EMBL c/o DESY	P14 (MX2)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	170.33	99.6	0.099	1	14.6	6.6		459122

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.052	98.3		0.29	1

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	FOURIER SYNTHESIS	THROUGHOUT	5LE5	2	170.33	459122	24018	99.6	0.17736	0.17549	0.18	0.21334	0.22	RANDOM	52.716

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]
3.38			-0.27		-3.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.427
r_dihedral_angle_4_deg	18.529
r_dihedral_angle_3_deg	15.755
r_long_range_B_refined	9.853
r_long_range_B_other	9.853
r_dihedral_angle_1_deg	7.281
r_scangle_other	3.275
r_scbond_it	2.27
r_scbond_other	2.269
r_mcangle_it	2.229
r_mcangle_other	2.229
r_angle_refined_deg	1.938
r_angle_other_deg	1.401
r_mcbond_it	1.361
r_mcbond_other	1.36
r_chiral_restr	0.125
r_bond_refined_d	0.019
r_gen_planes_refined	0.01
r_bond_other_d	0.007
r_gen_planes_other	0.005
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	48004
Nucleic Acid Atoms
Solvent Atoms	3595
Heterogen Atoms	211

Software

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