3ACP | pdb_00003acp

Crystal Structure of Yeast Rpn14, a Chaperone of the 19S Regulatory Particle of the Proteasome

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	PEG 3350, MgCl2, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.581	α = 90
b = 78.581	β = 90
c = 110.122	γ = 120

Symmetry
Space Group	P 64

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	Bruker DIP-6040		2008-02-13	M	SINGLE WAVELENGTH
2	2	x-ray	100	CCD	Bruker DIP-6040		2008-02-13	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9	SPring-8	BL44XU
2	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.97914, 0.9794, 0.96417	SPring-8	BL44XU

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	2	39.28	100	0.046	10.1	5.3		26081		1	32.09

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)
	2	2.11	100		0.405	2.1

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	MAD	THROUGHOUT	2	19.34	24720	1325	99.99	0.203	0.2	0.22	0.255	0.26	RANDOM	39.994

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]
-0.11	-0.05		-0.11		0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.605
r_dihedral_angle_4_deg	23.854
r_dihedral_angle_3_deg	18.381
r_dihedral_angle_1_deg	8.792
r_scangle_it	4.736
r_scbond_it	2.949
r_mcangle_it	2.202
r_angle_refined_deg	1.968
r_mcbond_it	1.24
r_chiral_restr	0.135

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.605
r_dihedral_angle_4_deg	23.854
r_dihedral_angle_3_deg	18.381
r_dihedral_angle_1_deg	8.792
r_scangle_it	4.736
r_scbond_it	2.949
r_mcangle_it	2.202
r_angle_refined_deg	1.968
r_mcbond_it	1.24
r_chiral_restr	0.135
r_bond_refined_d	0.021
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3266
Nucleic Acid Atoms
Solvent Atoms	82
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALA	data scaling
SHELX	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
MOSFLM	data reduction
SHARP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.