8IC9

Lys48-linked K48C-diubiquitin

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, HANGING DROP	4	277	38% 2-methyl-2,4-pentanediol and 50 mM sodium citrate (pH 4.0)

Crystal Properties
Matthews coefficient	Solvent content
1.91	35.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.79	α = 90
b = 31.191	β = 106.929
c = 25.272	γ = 88.65

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	PIXEL	DECTRIS EIGER X 16M		2021-07-19	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)	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	1.25	19.641	95.1	0.062	0.992	6.7	3.6		66682

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.25	1.27	93.6		0.554	0.911	2.7

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.25	19.641	66680	3360	95.071	0.188	0.1861	0.2188	22.291

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]
-1.427	0.758	-0.568	1.236	0.399	0.491

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.019
r_dihedral_angle_4_deg	14.018
r_dihedral_angle_3_deg	13.336
r_dihedral_angle_1_deg	7.175
r_lrange_other	5.088
r_lrange_it	5.087
r_scangle_it	4.631
r_scangle_other	4.629
r_mcangle_it	4.607
r_mcangle_other	4.591
r_scbond_other	3.959
r_scbond_it	3.958
r_mcbond_it	3.836
r_mcbond_other	3.824
r_rigid_bond_restr	3.196
r_angle_refined_deg	1.574
r_angle_other_deg	1.396
r_symmetry_nbd_refined	0.233
r_nbd_other	0.217
r_nbd_refined	0.212
r_symmetry_xyhbond_nbd_refined	0.187
r_symmetry_nbd_other	0.183
r_nbtor_refined	0.16
r_xyhbond_nbd_refined	0.143
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.079
r_symmetry_xyhbond_nbd_other	0.038
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2400
Nucleic Acid Atoms
Solvent Atoms	174
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing