8IA5

Small peptide enhances the binding of nutline-3a to N-terminal domain of MdmX

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7C3Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	0.1M HEPES pH6.0, 1.6M Ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.08	α = 90
b = 47.08	β = 90
c = 90.45	γ = 90

Symmetry
Space Group	P 43 21 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	PIXEL	DECTRIS EIGER2 X 16M		2020-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL02U1	0.9792	SSRF	BL02U1

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	1.93	26.81	98.8	0.068	1	24.1		8075

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.93	5.23			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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	NONE	1.93	26.81	8056	430	98.629	0.214	0.2101	0.2838	46.762

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]
-0.067			-0.067		0.133

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.196
r_dihedral_angle_6_deg	15.55
r_lrange_it	15.242
r_lrange_other	15.142
r_dihedral_angle_2_deg	9.54
r_dihedral_angle_1_deg	7.229
r_scangle_it	7.006
r_scangle_other	7
r_mcangle_other	6.13
r_mcangle_it	6.125
r_scbond_it	4.63
r_scbond_other	4.626
r_mcbond_other	4.419
r_mcbond_it	4.413
r_angle_refined_deg	1.454
r_symmetry_nbd_refined	0.543
r_angle_other_deg	0.5
r_nbd_refined	0.327
r_symmetry_nbd_other	0.244
r_symmetry_xyhbond_nbd_refined	0.214
r_nbtor_refined	0.198
r_nbd_other	0.19
r_xyhbond_nbd_refined	0.18
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.077
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	767
Nucleic Acid Atoms
Solvent Atoms	62
Heterogen Atoms	58

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data scaling
xia2	data reduction
MrBUMP	phasing
HKL-3000	data collection
PDB_EXTRACT	data extraction
Aimless	data scaling