5K1C | pdb_00005k1c

Crystal structure of the UAF1/WDR20/USP12 complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5K16	5K16, 5K19 and 5K1A
experimental model	PDB	5K19	5K16, 5K19 and 5K1A
experimental model	PDB	5K1A	5K16, 5K19 and 5K1A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	277	0.1 M MES, 1.3 M ammonium phosphate dibasic

Crystal Properties
Matthews coefficient	Solvent content
4.58	73.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 217.903	α = 90
b = 217.903	β = 90
c = 223.819	γ = 120

Symmetry
Space Group	P 61 2 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	ADSC QUANTUM 315r		2015-03-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	1.0	ALS	8.2.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	3	50.01	97.8	0.105	0.109	27.4	11.3		58534

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.05	98.7		1.5	9.2

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	5K16, 5K19 and 5K1A	3	50.01	58534	3014	97.69	0.23239	0.23038	0.24	0.27083	0.28	RANDOM	97.881

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]
-0.17	-0.09		-0.17		0.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.818
r_dihedral_angle_3_deg	17.288
r_dihedral_angle_4_deg	16.421
r_long_range_B_refined	15.64
r_long_range_B_other	15.639
r_scangle_other	11.188
r_mcangle_it	10.259
r_mcangle_other	10.258
r_dihedral_angle_1_deg	8.651
r_scbond_it	7.166
r_scbond_other	7.165
r_mcbond_it	6.633
r_mcbond_other	6.63
r_angle_other_deg	3.832
r_angle_refined_deg	1.737
r_chiral_restr	0.095
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_gen_planes_other	0.005
r_bond_other_d
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9541
Nucleic Acid Atoms
Solvent Atoms	75
Heterogen Atoms	17

Software

Software
Software Name	Purpose
REFMAC	refinement
Coot	model building
PHASER	phasing
HKL-2000	data reduction
HKL-2000	data scaling