9Y8V | pdb_00009y8v

Crystal structure of the Kelch domain of human KLHL12 with compound 10q

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
1.89	34.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.571	α = 90
b = 79.571	β = 90
c = 76.631	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	PIXEL	DECTRIS EIGER2 S 9M		2023-07-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	0.98	ALS	8.2.1

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	1.271	56.329	96.4	0.051	1	25.2	10.7		59437

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	1.271	1.38	50.4		1.06	0.404	0.7	1.7

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	THROUGHOUT	1.271	56.329	59437	2836	91.234	0.162	0.1604	0.1894	0.1994	0.2155	12.324

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]
1.261			1.261		-2.523

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.917
r_dihedral_angle_3_deg	11.551
r_lrange_it	10.9
r_lrange_other	9.54
r_dihedral_angle_2_deg	8.815
r_dihedral_angle_1_deg	7.838
r_scangle_it	5.694
r_scangle_other	5.692
r_mcangle_other	4.581
r_mcangle_it	4.579
r_scbond_it	3.833
r_scbond_other	3.823
r_rigid_bond_restr	3.523
r_mcbond_it	2.954
r_mcbond_other	2.951
r_angle_refined_deg	1.7
r_angle_other_deg	0.641
r_symmetry_nbd_refined	0.274
r_symmetry_xyhbond_nbd_other	0.267
r_nbd_other	0.23
r_symmetry_xyhbond_nbd_refined	0.22
r_xyhbond_nbd_refined	0.214
r_symmetry_nbd_other	0.204
r_nbd_refined	0.202
r_nbtor_refined	0.181
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.091
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2166
Nucleic Acid Atoms
Solvent Atoms	274
Heterogen Atoms	40

Software

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