9Y8O | pdb_00009y8o

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

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	35.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.67	α = 90
b = 79.67	β = 90
c = 77.26	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		2021-09-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97857	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	1.286	55.53	91.4	0.09	0.999	10.2	12.8		63553

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	1.286	1.31	100		0.471	0.98	4.2	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	FREE R-VALUE	1.286	55.525	63553	3122	99.958	0.156	0.1547	0.1548	0.1772	0.1771	13.755

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]
0.189			0.189		-0.377

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	20.728
r_dihedral_angle_6_deg	16.266
r_dihedral_angle_3_deg	10.324
r_dihedral_angle_1_deg	8.089
r_lrange_it	4.215
r_lrange_other	3.893
r_scangle_it	2.834
r_scangle_other	2.833
r_angle_refined_deg	1.871
r_scbond_it	1.851
r_scbond_other	1.851
r_dihedral_angle_other_2_deg	1.572
r_mcangle_it	1.564
r_mcangle_other	1.563
r_mcbond_it	0.983
r_mcbond_other	0.978
r_angle_other_deg	0.671
r_symmetry_xyhbond_nbd_refined	0.289
r_nbd_refined	0.216
r_symmetry_nbd_other	0.186
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.162
r_nbd_other	0.158
r_symmetry_xyhbond_nbd_other	0.103
r_chiral_restr	0.1
r_symmetry_nbd_refined	0.097
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	2186
Nucleic Acid Atoms
Solvent Atoms	348
Heterogen Atoms	33

Software

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