6W2G | pdb_00006w2g

Crystal Structure of Y188G Variant of the Internal UBA Domain of HHR23A in Monoclinic Unit Cell

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		P43 UBA-1 Y188G Structure Solved by Sulfur SAD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2M Ammonium sulfate, 0.1M Phosphate-citrate pH 4.2, 40%(v/v) Ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
1.76	29.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 29.49	α = 90
b = 40.08	β = 91.389
c = 32.893	γ = 90

Symmetry
Space Group	P 1 21 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		2020-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	1	SSRL	BL9-2

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	1.1	33.88	94.77	0.01716	0.01868	0.007273	1	56.13	6.2		29568			6.64

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.1	1.139	81.04		0.07858	0.0884	0.0396	0.997	16.63	4.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	P43 UBA-1 Y188G Structure Solved by Sulfur SAD	1.1	32.88	1.45	29568	1763	94.77	0.1399	0.1391	0.14	0.1527	0.15	9.33

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.472
f_angle_d	1.0356
f_chiral_restr	0.0766
f_bond_d	0.0083
f_plane_restr	0.0068

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	745
Nucleic Acid Atoms
Solvent Atoms	75
Heterogen Atoms	12

Software

Software
Software Name	Purpose
Blu-Ice	data collection
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	model building
Coot	model building
PHENIX	refinement

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.