7C44 | pdb_00007c44

Crystal structure of the p53-binding domain of human MdmX protein in complex with Nutlin3a

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6Q9W	6Q9W, 6V4F
experimental model	PDB	6V4F	6Q9W, 6V4F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	20% v/v Tacsimate pH 7.0, 0.1 M HEPES sodium salt pH 7.5, 2% (w/v) PEG 200

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.47	α = 90
b = 47.47	β = 90
c = 91.19	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 EIGER X 16M		2020-01-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.979	SSRF	BL17U1

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	1.632	42.148	100	0.06	0.062	0.013	1	28.4	22.7		13154

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	1.65	1.94	100		0.854	0.882	0.215	0.884		16.4

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6Q9W, 6V4F	1.65	25.611	13154	675	99.75	0.21	0.2075	0.22	0.2647	0.27	36.364

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]
0.715			0.715		-1.431

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.691
r_dihedral_angle_4_deg	24.958
r_dihedral_angle_3_deg	15.726
r_lrange_it	8.018
r_lrange_other	8.014
r_dihedral_angle_1_deg	7.156
r_scangle_other	6.798
r_scangle_it	6.57
r_scbond_it	4.648
r_scbond_other	4.643
r_mcangle_it	4.224
r_mcangle_other	4.22
r_mcbond_it	3.173
r_mcbond_other	3.138
r_angle_other_deg	2.195
r_angle_refined_deg	1.699
r_nbd_refined	0.225
r_symmetry_nbd_other	0.222
r_nbd_other	0.188
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.178
r_symmetry_nbd_refined	0.176
r_symmetry_xyhbond_nbd_refined	0.154
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.083
r_bond_other_d	0.034
r_gen_planes_other	0.013
r_bond_refined_d	0.012
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	773
Nucleic Acid Atoms
Solvent Atoms	26
Heterogen Atoms	58

Software

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