9Y8M | pdb_00009y8m

Crystal structure of the Kelch domain of human KLHL12 with compound 8i

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VPJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	0.1M Bis-Tris pH 5.5, 0.2M MgCl2 and 25% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.891	α = 90
b = 79.891	β = 90
c = 76.67	γ = 90

Symmetry
Space Group	P 41 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	CCD	MARMOSAIC 300 mm CCD		2021-12-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.98	APS	21-ID-D

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	1.33	55.32	91.4	0.071	0.998	22.8	12.8		52105

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	1.33	1.36	100		0.193	0.988	11.4	12.9

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	THROUGHOUT	1.334	45.521	52035	2657	91.378	0.164	0.1635	0.1635	0.1785	0.1786	11.974

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]
0.126			0.126		-0.253

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.273
r_dihedral_angle_2_deg	11.546
r_dihedral_angle_3_deg	11.292
r_dihedral_angle_1_deg	7.961
r_lrange_it	5.057
r_scangle_it	3.176
r_scbond_it	2.104
r_mcangle_it	2.098
r_angle_refined_deg	2.07
r_mcbond_it	1.297
r_nbtor_refined	0.304
r_symmetry_xyhbond_nbd_refined	0.282
r_symmetry_nbd_refined	0.224
r_nbd_refined	0.204
r_xyhbond_nbd_refined	0.191
r_chiral_restr	0.127
r_gen_planes_refined	0.013
r_bond_refined_d	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2163
Nucleic Acid Atoms
Solvent Atoms	364
Heterogen Atoms	25

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing