8BZL | pdb_00008bzl

Human 20S Proteasome in complex with peptide activator peptide BLM42

X-RAY DIFFRACTION

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Serial Crystallography (SX)

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
2.37	48.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.915	α = 90
b = 203.262	β = 90
c = 316.421	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 EIGER X 16M		2018-04-04	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)

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1		fixed target

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.14	107.181	94.5	0.1366	0.1474	0.055	0.995	6.65	7.1		327921

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.14	2.295	62.9		1.4184	1.5254	0.5585	0.635	1.53	7.41	16397

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 (All)	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	2.14	107.123	327919	16354	81.566	0.198	0.1962	0.1961	0.2261	0.226	RANDOM	47.647

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]
-0.295			0.477		-0.182

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.254
r_dihedral_angle_6_deg	13.107
r_lrange_it	6.91
r_dihedral_angle_1_deg	6.118
r_dihedral_angle_2_deg	3.52
r_scangle_it	1.371
r_mcangle_it	1.188
r_angle_refined_deg	0.892
r_scbond_it	0.826
r_mcbond_it	0.66
r_nbtor_refined	0.296
r_symmetry_nbd_refined	0.196
r_nbd_refined	0.193
r_symmetry_xyhbond_nbd_refined	0.131
r_xyhbond_nbd_refined	0.124
r_ncsr_local_group_4	0.082
r_chiral_restr	0.074
r_ncsr_local_group_8	0.066
r_ncsr_local_group_7	0.062
r_ncsr_local_group_9	0.061
r_ncsr_local_group_1	0.055
r_ncsr_local_group_6	0.051
r_ncsr_local_group_2	0.05
r_ncsr_local_group_3	0.05
r_ncsr_local_group_5	0.049
r_metal_ion_refined	0.047
r_ncsr_local_group_10	0.046
r_ncsr_local_group_12	0.043
r_ncsr_local_group_11	0.042
r_ncsr_local_group_13	0.041
r_ncsr_local_group_14	0.02
r_bond_refined_d	0.003
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	47032
Nucleic Acid Atoms
Solvent Atoms	3404
Heterogen Atoms	236

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data processing
XDS	data reduction
Aimless	data scaling
Coot	model building
MOLREP	phasing