4ASC | pdb_00004asc

Crystal structure of the Kelch domain of human KBTBD5

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				0.1 M CITRATE PH 5.3, 20%(W/V) PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.33	α = 90
b = 64.95	β = 90
c = 89.2	γ = 90

Symmetry
Space Group	P 21 21 21

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		2012-03-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1		Diamond	I04-1

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	1.78	39.89	99.9	0.07	13.9	6.2		34642		2	18.12

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	1.78	1.82	99.9		0.56	3.1	6.4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2WOZ	1.78	52.51	32847	1744	99.75	0.18053	0.17815	0.18	0.22623	0.23	RANDOM	18.116

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]
0.79			-0.18		-0.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.134
r_dihedral_angle_4_deg	21.679
r_dihedral_angle_3_deg	13.801
r_dihedral_angle_1_deg	6.924
r_scangle_it	6.307
r_mcangle_it	3.555
r_scbond_it	2.41
r_mcbond_it	2.293
r_angle_refined_deg	1.661
r_angle_other_deg	0.904
r_symmetry_vdw_refined	0.364
r_symmetry_vdw_other	0.295
r_nbd_refined	0.268
r_nbd_other	0.23
r_nbtor_refined	0.185
r_symmetry_hbond_refined	0.177
r_nbtor_other	0.126
r_chiral_restr	0.106
r_xyhbond_nbd_refined	0.106
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_mcbond_other	0.003
r_bond_other_d	0.001
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_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	2371
Nucleic Acid Atoms
Solvent Atoms	227
Heterogen Atoms	8

Software

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