9Y8N | pdb_00009y8n

Crystal structure of the Kelch domain of human KLHL12 with compound 8m

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
1.83	32.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.633	α = 90
b = 79.633	β = 90
c = 74.382	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		2022-03-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.99	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	1.308	33.72	99.2	0.132	0.997	8.4	11.4		45864

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	1.308	1.33	78.6		0.561	0.382	1	10.7

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	1.308	33.72	45864	2280	78.749	0.161	0.1586	0.1671	0.2038	0.203	14.441

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]
0.497			0.497		-0.993

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.293
r_dihedral_angle_3_deg	12.09
r_dihedral_angle_2_deg	10.66
r_lrange_it	9.802
r_lrange_other	8.007
r_dihedral_angle_1_deg	7.721
r_scangle_it	5.152
r_scangle_other	5.15
r_rigid_bond_restr	3.925
r_mcangle_other	3.901
r_mcangle_it	3.895
r_scbond_it	3.577
r_scbond_other	3.576
r_mcbond_it	2.637
r_mcbond_other	2.611
r_angle_refined_deg	1.907
r_angle_other_deg	0.703
r_symmetry_xyhbond_nbd_refined	0.337
r_xyhbond_nbd_refined	0.269
r_symmetry_nbd_refined	0.234
r_nbd_other	0.228
r_nbd_refined	0.208
r_symmetry_nbd_other	0.189
r_symmetry_xyhbond_nbd_other	0.182
r_nbtor_refined	0.175
r_chiral_restr	0.102
r_symmetry_nbtor_other	0.086
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
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	308
Heterogen Atoms	23

Software

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