6HD0 | pdb_00006hd0

Common mode of remodeling AAA ATPases p97/CDC48 by their disassembly cofactors ASPL/PUX1

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1S3S	1S3S, 5IFS
experimental model	PDB	5IFS	1S3S, 5IFS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	6% (v/v) PEG1500, 0.2M sodium acetate, 0.1M Hepes pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
3.5	64.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 185.12	α = 90
b = 185.12	β = 90
c = 122.426	γ = 120

Symmetry
Space Group	P 31

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 PILATUS3 6M		2014-08-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91841	BESSY	14.1

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	3.728	48.98	90.7	0.306	0.34	0.148	0.983	6.2	5.3		28980

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.88	4.03	98.1		0.2686	0.324	0.75

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	1S3S, 5IFS	3.728	48.98	26254	2606	58.94	0.2117	0.2077	0.21	0.2529	0.25	RANDOM	123.914

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]
-50.75			-50.75		101.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.589
r_dihedral_angle_4_deg	11.934
r_dihedral_angle_3_deg	11.257
r_dihedral_angle_1_deg	4.187
r_angle_refined_deg	1.168
r_angle_other_deg	1.04
r_chiral_restr	0.033
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.589
r_dihedral_angle_4_deg	11.934
r_dihedral_angle_3_deg	11.257
r_dihedral_angle_1_deg	4.187
r_angle_refined_deg	1.168
r_angle_other_deg	1.04
r_chiral_restr	0.033
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	24272
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	162

Software

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

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.