2Z5C

Crystal Structure of a Novel Chaperone Complex for Yeast 20S Proteasome Assembly

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Z5B	PDB ENTRY 2Z5B; PDB ENTRY 1RYP chain E
experimental model	PDB	1RYP	PDB ENTRY 2Z5B; PDB ENTRY 1RYP chain E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	0.1M Tris-HCl, 8%(v/v) ethyleneglycol, 12%(w/v) PEG 8000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.29	62.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 158.687	α = 90
b = 159.181	β = 90
c = 65.035	γ = 90

Symmetry
Space Group	P 21 21 2

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		2007-04-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9000	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	2.9	50.38	99.8	0.08	20	6.3		37091		-3

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)
	2.9	3	99.9		0.35		6.4

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	PDB ENTRY 2Z5B; PDB ENTRY 1RYP chain E	2.9	50.38	35178	1859	99.44	0.2513	0.24962	0.24	0.28334	0.28	RANDOM	66.851

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]
2.61			2.45		-5.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.341
r_dihedral_angle_3_deg	23.623
r_dihedral_angle_4_deg	21.918
r_dihedral_angle_1_deg	7.846
r_scangle_it	2.693
r_angle_refined_deg	1.757
r_scbond_it	1.634
r_mcangle_it	1.602
r_mcbond_it	0.9
r_symmetry_vdw_refined	0.402
r_symmetry_hbond_refined	0.363
r_nbtor_refined	0.319
r_nbd_refined	0.253
r_xyhbond_nbd_refined	0.186
r_chiral_restr	0.115
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6598
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing