9Y8Q | pdb_00009y8q

Crystal structure of the Kelch domain of human KLHL12 with compound 9e

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
1.91	35.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.95	α = 90
b = 79.95	β = 90
c = 76.8	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	Beryllium Lenses	2021-07-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97872	APS	21-ID-G

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	1.2	35.78	100	0.071	0.999	19	14.1		78068

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	1.2	1.22	99.8		0.366	0.965	5.8	13.7

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	1.2	35.78	78068	4014	99.99	0.134	0.1326	0.1415	0.1521	0.1591	11.099

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]
-0.482			-0.482		0.964

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	20.664
r_dihedral_angle_6_deg	16.769
r_dihedral_angle_3_deg	10.907
r_lrange_it	8.312
r_dihedral_angle_1_deg	8.244
r_lrange_other	6.769
r_rigid_bond_restr	4.586
r_scangle_it	4.04
r_scangle_other	4.04
r_mcangle_other	3.132
r_mcangle_it	3.128
r_scbond_other	2.813
r_scbond_it	2.812
r_dihedral_angle_other_2_deg	2.028
r_mcbond_it	1.987
r_mcbond_other	1.973
r_angle_refined_deg	1.94
r_angle_other_deg	0.728
r_symmetry_xyhbond_nbd_refined	0.317
r_nbd_refined	0.213
r_symmetry_nbd_refined	0.205
r_symmetry_nbd_other	0.19
r_xyhbond_nbd_refined	0.19
r_nbd_other	0.178
r_nbtor_refined	0.177
r_chiral_restr	0.114
r_symmetry_nbtor_other	0.088
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2163
Nucleic Acid Atoms
Solvent Atoms	362
Heterogen Atoms	34

Software

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