8E7O | pdb_00008e7o

CRYSTAL STRUCTURE OF LYS48-LINKED TETRAUBIQUITIN

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AAR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295.15	25% w/v PEG 3350, 0.2M ammonium sulfate, 0.1M Bis-Tris pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.839	α = 90
b = 77.164	β = 90
c = 135.823	γ = 90

Symmetry
Space Group	C 2 2 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		2019-06-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.97918	APS	24-ID-E

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.7	67.911	99.3	1	1.27	7.8		34404

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	1.7	1.73	96.8		0.355		7.3

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1AAR	1.7	67.911	34167	1742	99.265	0.16	0.1567	0.16	0.2206	0.23	50.053

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]
-0.61			0.338		0.272

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.038
r_scangle_it	15.869
r_scbond_it	15.47
r_dihedral_angle_3_deg	15.336
r_lrange_it	14.088
r_dihedral_angle_1_deg	8.284
r_mcangle_it	8.025
r_rigid_bond_restr	7.753
r_mcbond_it	7.721
r_dihedral_angle_2_deg	7.656
r_angle_refined_deg	2.19
r_nbtor_refined	0.253
r_symmetry_xyhbond_nbd_refined	0.224
r_symmetry_nbd_refined	0.16
r_chiral_restr	0.153
r_nbd_refined	0.148
r_ncsr_local_group_1	0.145
r_ncsr_local_group_5	0.143
r_xyhbond_nbd_refined	0.137
r_ncsr_local_group_4	0.135
r_ncsr_local_group_6	0.129
r_ncsr_local_group_3	0.128
r_ncsr_local_group_2	0.104
r_bond_refined_d	0.011
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2406
Nucleic Acid Atoms
Solvent Atoms	160
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
CRANK2	phasing