5VK1 | pdb_00005vk1

Crystal structure of human MDM4 in complex with a 12-mer lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3EQY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	294	30% 2-propanol, 30% PEG 3350, and 100 mM Tris-HCl pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.294	α = 76.72
b = 47.73	β = 89.92
c = 93.394	γ = 72.6

Symmetry
Space Group	P 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 PILATUS 6M		2016-11-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.97946	SSRL	BL12-2

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	2.69	50	86	0.132	10.3	1.9		16330

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	2.69	2.75	78.7		0.614	1.1	1.8	704

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	3eqy	2.69	50	15495	835	85.47	0.28145	0.2787	0.28	0.33486	0.34	RANDOM	54.37

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]
-0.43	2.88	0.01	0.78	-1.52	0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.23
r_dihedral_angle_3_deg	21.641
r_dihedral_angle_4_deg	16.554
r_dihedral_angle_1_deg	5.751
r_angle_refined_deg	1.32
r_angle_other_deg	1.031
r_long_range_B_refined	0.705
r_long_range_B_other	0.705
r_mcangle_it	0.118
r_mcangle_other	0.118
r_scangle_other	0.083
r_mcbond_it	0.079
r_mcbond_other	0.079
r_chiral_restr	0.065
r_scbond_it	0.044
r_scbond_other	0.044
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_gen_planes_other	0.004
r_bond_other_d	0.003
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	6008
Nucleic Acid Atoms
Solvent Atoms	27
Heterogen Atoms

Software

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