9Y8R | pdb_00009y8r

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

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	34.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.78	α = 90
b = 79.78	β = 90
c = 76.37	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	55.23	100	0.086	0.997	18.3	13		56571

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	1.37	100		0.245	0.984	8.2	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	1.334	55.229	56571	2885	99.993	0.161	0.1599	0.1604	0.1727	0.1596	12.048

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]
-0.149			-0.149		0.298

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.24
r_dihedral_angle_3_deg	10.985
r_dihedral_angle_2_deg	8.242
r_dihedral_angle_1_deg	8.052
r_lrange_it	4.096
r_lrange_other	3.618
r_scangle_it	2.295
r_scangle_other	2.294
r_angle_refined_deg	1.872
r_mcangle_it	1.736
r_mcangle_other	1.736
r_scbond_it	1.489
r_scbond_other	1.489
r_mcbond_it	1.053
r_mcbond_other	1.043
r_angle_other_deg	0.671
r_symmetry_nbd_refined	0.236
r_xyhbond_nbd_refined	0.229
r_symmetry_xyhbond_nbd_other	0.225
r_nbd_refined	0.212
r_symmetry_nbd_other	0.197
r_symmetry_xyhbond_nbd_refined	0.194
r_nbtor_refined	0.179
r_nbd_other	0.171
r_chiral_restr	0.096
r_symmetry_nbtor_other	0.089
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
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	357
Heterogen Atoms	25

Software

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