2VPJ

Crystal structure of the Kelch domain of human KLHL12

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DYH	PDB ENTRY 2DYH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.6		0.2M AMMONIUM ACETATE, 0.1M SODIUM ACETATE PH4.6, 30% PEG4K

Crystal Properties
Matthews coefficient	Solvent content
1.77	30.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.637	α = 90
b = 61.546	β = 111.75
c = 45.523	γ = 90

Symmetry
Space Group	P 1 21 1

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	MARRESEARCH		2008-01-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA		SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.85	42.3	99.4	0.09	10.6	4.3		19527			23.09

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.95	96.1		0.63	2	3.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2DYH	1.85	42.3	18504	990	99.2	0.164	0.161	0.222	RANDOM	23.13

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]
0.21		-0.31	-1.58		1.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.538
r_dihedral_angle_4_deg	18.535
r_dihedral_angle_3_deg	13.398
r_scangle_it	7.668
r_dihedral_angle_1_deg	7.581
r_scbond_it	5.868
r_mcangle_it	3.674
r_mcbond_it	2.429
r_angle_refined_deg	1.571
r_angle_other_deg	0.989
r_symmetry_vdw_other	0.298
r_nbd_other	0.249
r_nbd_refined	0.189
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.157
r_symmetry_vdw_refined	0.144
r_symmetry_hbond_refined	0.127
r_nbtor_other	0.119
r_chiral_restr	0.096
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2184
Nucleic Acid Atoms
Solvent Atoms	132
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing