8XI7 | pdb_00008xi7

The Crystal Structure of UCHL1 from Biortus.

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4JKJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	2.1M ammonium sulfate, 2% PEG 400, 100mM HEPES, pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.216	α = 90
b = 109.216	β = 90
c = 79.379	γ = 90

Symmetry
Space Group	P 4 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	PIXEL	DECTRIS EIGER X 9M		2022-12-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.95374	CLSI	08ID-1

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	1.95	48.84	100	0.09	20.9	19.2		35583

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)
1	1.95	2			1.056

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	1.95	48.84	35556	1855	99.947	0.196	0.1939	0.2	0.2311	0.24	40.415

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]
1.41			1.41		-2.819

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.472
r_dihedral_angle_3_deg	13.394
r_lrange_other	8.009
r_lrange_it	8.006
r_dihedral_angle_1_deg	5.914
r_scangle_other	5.855
r_scangle_it	5.85
r_dihedral_angle_2_deg	4.821
r_mcangle_it	4.342
r_mcangle_other	4.341
r_scbond_other	3.607
r_scbond_it	3.604
r_mcbond_it	2.857
r_mcbond_other	2.856
r_angle_refined_deg	1.06
r_angle_other_deg	0.361
r_nbd_refined	0.204
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.173
r_symmetry_xyhbond_nbd_refined	0.168
r_xyhbond_nbd_refined	0.15
r_nbd_other	0.149
r_symmetry_nbd_refined	0.115
r_ncsr_local_group_1	0.096
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.054
r_symmetry_xyhbond_nbd_other	0.049
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3470
Nucleic Acid Atoms
Solvent Atoms	231
Heterogen Atoms	14

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing