6TG8 | pdb_00006tg8

Crystal structure of the Kelch domain in complex with 11 amino acid peptide (model of the ETGE loop)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZGK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	289	1.8 M sodium acetate pH 7.0, 0.1 M Bis-Tris propane pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
3.18	61.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.296	α = 90
b = 75.296	β = 90
c = 127.539	γ = 120

Symmetry
Space Group	P 31 2 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	PIXEL	DECTRIS PILATUS 2M		2019-10-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	1.0	ELETTRA	5.2R

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	2.45	65.208	99.5	0.11	40.66	18.1		11948

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	2.7	2.8			0.614

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1zgk	2.75	17	11310	560	99.49	0.185	0.181	0.19	0.2584	0.26	69.133

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]
-0.06	-0.03		-0.06		0.196

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.296
r_dihedral_angle_4_deg	19.114
r_dihedral_angle_3_deg	16.645
r_lrange_it	10.99
r_lrange_other	10.988
r_dihedral_angle_1_deg	8.742
r_scangle_it	8.655
r_scangle_other	8.647
r_mcangle_it	7.247
r_mcangle_other	7.246
r_scbond_it	5.518
r_scbond_other	5.494
r_mcbond_it	4.891
r_mcbond_other	4.874
r_angle_refined_deg	1.499
r_angle_other_deg	1.212
r_symmetry_nbd_refined	0.243
r_symmetry_xyhbond_nbd_refined	0.215
r_nbd_refined	0.201
r_symmetry_nbd_other	0.194
r_nbtor_refined	0.166
r_nbd_other	0.157
r_xyhbond_nbd_refined	0.129
r_symmetry_nbtor_other	0.088
r_chiral_restr	0.052
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2302
Nucleic Acid Atoms
Solvent Atoms	9
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
Aimless	data scaling
AMoRE	phasing