9Y8S | pdb_00009y8s

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

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	35.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.79	α = 90
b = 79.79	β = 90
c = 76.89	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		2021-07-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.98004	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	56.484	100	0.067	0.994	19.7	12.6		63441

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	1.29	1.31	100		0.357	0.967	6.5	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	56.484	63441	3198	99.948	0.152	0.1507	0.151	0.1701	0.1702	13.078

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]
-0.256			-0.256		0.511

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	21.53
r_dihedral_angle_6_deg	16.512
r_dihedral_angle_3_deg	10.08
r_dihedral_angle_1_deg	8.113
r_dihedral_angle_other_2_deg	5.244
r_lrange_it	4.253
r_lrange_other	3.784
r_scangle_it	2.793
r_scangle_other	2.792
r_angle_refined_deg	1.784
r_scbond_it	1.784
r_scbond_other	1.782
r_mcangle_it	1.503
r_mcangle_other	1.503
r_mcbond_it	0.935
r_mcbond_other	0.935
r_angle_other_deg	0.64
r_nbd_refined	0.205
r_symmetry_xyhbond_nbd_refined	0.198
r_symmetry_nbd_other	0.188
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.16
r_nbd_other	0.137
r_symmetry_nbd_refined	0.119
r_chiral_restr	0.092
r_symmetry_nbtor_other	0.087
r_bond_refined_d	0.011
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	366
Heterogen Atoms	33

Software

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