7OZT | pdb_00007ozt

Nanobodies restore stability to cancer-associated mutants of tumor suppressor protein p16INK4a

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BI7	1BI7, 3OGO
experimental model	PDB	3OGO	1BI7, 3OGO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	Molecular Dimensions Morpheus screen condition G4

Crystal Properties
Matthews coefficient	Solvent content
1.91	35.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.119	α = 90
b = 182.931	β = 90
c = 65.225	γ = 90

Symmetry
Space Group	C 2 2 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	PIXEL	DECTRIS PILATUS3 6M		2018-02-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97622	Diamond	I03

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	1.74	91.47	100	0.101	0.119	0.061	0.998	9.2	6.8		26446

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	1.74	1.77			0.878	1.058	0.582	0.361		6.2

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1BI7, 3OGO	1.74	91.465	26427	930	99.996	0.181	0.1798	0.19	0.2086	0.22	Random selection	27.959

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]
1.175			-1.038		-0.137

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.079
r_dihedral_angle_4_deg	18.676
r_dihedral_angle_3_deg	15.269
r_lrange_it	6.946
r_lrange_other	6.927
r_dihedral_angle_1_deg	6.884
r_scangle_it	5.461
r_scangle_other	5.459
r_scbond_it	3.382
r_scbond_other	3.38
r_mcangle_other	3.186
r_mcangle_it	3.184
r_angle_refined_deg	2.081
r_mcbond_it	2.006
r_mcbond_other	1.979
r_angle_other_deg	1.41
r_nbd_other	0.249
r_nbd_refined	0.206
r_xyhbond_nbd_refined	0.202
r_symmetry_xyhbond_nbd_refined	0.194
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.16
r_symmetry_nbd_refined	0.158
r_chiral_restr	0.102
r_symmetry_nbtor_other	0.086
r_bond_refined_d	0.016
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1854
Nucleic Acid Atoms
Solvent Atoms	90
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
PHASER	phasing
Coot	model building