9QY8 | pdb_00009qy8

Crystal structure of apoform human USP18

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5CHT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	0.2 M sodium citrate tribasic dihydrate, 0.1 M Bis-Tris propane, pH 7.5, 20 % (w/v) PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.41	49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.868	α = 79.32
b = 71.775	β = 76.283
c = 73.063	γ = 89.882

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	100	PIXEL	DECTRIS PILATUS 6M-F		2023-12-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9537	Diamond	I04

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	1.919	39.593	97.9	0.071	0.996	17.9	3.6		69489

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	1.92	1.95			2.455	0.342

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.919	39.593	69138	2020	97.436	0.206	0.2048	0.2126	0.2601	0.2661	55.037

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]
1.879	-0.944	-0.39	-2.278	-0.261	0.084

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.836
r_dihedral_angle_6_deg	14.948
r_dihedral_angle_2_deg	9.959
r_lrange_it	7.894
r_lrange_other	7.887
r_dihedral_angle_1_deg	7.28
r_scangle_it	6.256
r_scangle_other	6.255
r_mcangle_it	5.157
r_mcangle_other	5.156
r_scbond_it	4.46
r_scbond_other	4.459
r_mcbond_it	3.746
r_mcbond_other	3.746
r_angle_refined_deg	1.724
r_angle_other_deg	0.61
r_symmetry_nbd_refined	0.256
r_symmetry_xyhbond_nbd_other	0.252
r_nbd_other	0.237
r_nbd_refined	0.22
r_symmetry_nbd_other	0.196
r_symmetry_xyhbond_nbd_refined	0.189
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.171
r_ncsr_local_group_1	0.101
r_symmetry_nbtor_other	0.089
r_chiral_restr	0.087
r_ncsr_local_group_2	0.057
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4829
Nucleic Acid Atoms
Solvent Atoms	223
Heterogen Atoms	1904

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing