8P9C | pdb_00008p9c

Crystal structure of p63-p73 heterotetramer (tetramerisation domain) in complex with darpin 1810 F11

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6FP7
experimental model	PDB	5HOB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293.15	0.2M ammonium acetate, 25% PEG3350, 0.1M HEPES pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.024	α = 90
b = 60.312	β = 100.26
c = 53.576	γ = 90

Symmetry
Space Group	C 1 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 EIGER X 16M		2019-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.00000	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.76	48.73	96.7	0.049	0.063	0.031	0.997	12.2	4		25297

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.76	1.82			0.392	0.484	0.241	0.899	2.1	4.1

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 (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	1.76	48.73	24099	1197	96.44	0.17184	0.16991	0.18	0.21012	0.22	RANDOM	34.202

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]
-0.58		-0.11	0.96		-0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.46
r_dihedral_angle_4_deg	15.37
r_dihedral_angle_3_deg	14.462
r_long_range_B_refined	6.698
r_long_range_B_other	6.696
r_dihedral_angle_1_deg	6.483
r_scangle_other	4.374
r_mcangle_other	2.947
r_mcangle_it	2.946
r_scbond_it	2.784
r_scbond_other	2.782
r_mcbond_it	1.88
r_mcbond_other	1.874
r_angle_refined_deg	1.47
r_angle_other_deg	1.432
r_chiral_restr	0.094
r_bond_refined_d	0.016
r_gen_planes_refined	0.013
r_gen_planes_other	0.003
r_bond_other_d	0.001
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	2047
Nucleic Acid Atoms
Solvent Atoms	164
Heterogen Atoms	16

Software

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