9BKR

Crystal structure of the Human TRIP12 WWE domain (isoform 2) in complex with ATP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6MIW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	291	25 % P3350, 0.2 M Mg Cl, 0.1 M Tris pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
1.85	33.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.351	α = 90
b = 33.492	β = 90
c = 66.081	γ = 90

Symmetry
Space Group	P 21 21 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 EIGER2 X 16M		2022-12-09	M	SINGLE WAVELENGTH

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

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	1.4	50	97.9	0.128	0.134	0.039	0.998	7.9	12.2		13611

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	1.4	1.42	78.2		0.724	0.843	0.407	0.126		4.5

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.4	33.04	12941	630	97.47	0.16416	0.16196	0.20764	RANDOM	20.478

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]
0.23			0.3		-0.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.174
r_long_range_B_refined	13.444
r_long_range_B_other	12.889
r_scangle_other	9.402
r_mcangle_other	7.792
r_mcangle_it	7.786
r_dihedral_angle_1_deg	6.52
r_dihedral_angle_2_deg	6.502
r_scbond_it	6.345
r_scbond_other	6.336
r_mcbond_it	5.321
r_mcbond_other	5.232
r_rigid_bond_restr	3.346
r_angle_refined_deg	1.356
r_angle_other_deg	0.514
r_chiral_restr	0.079
r_gen_planes_refined	0.009
r_bond_refined_d	0.008
r_gen_planes_other	0.004
r_bond_other_d	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	595
Nucleic Acid Atoms
Solvent Atoms	54
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
HKL-3000	data reduction
PHASER	phasing