7AI0 | pdb_00007ai0

Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 1)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		MDM2-E2-Ub complex

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	292	0.1 M Tris, 0.075 M NaOAc, 0.1 M NaCl, 15 % w/v PEG Smear Medium

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 129.531	α = 90
b = 129.531	β = 90
c = 70.751	γ = 120

Symmetry
Space Group	P 61

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-F		2018-03-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91587	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.559	70.75	100	0.999	13.8	17.3		95993

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	1.56	1.59			0.518

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	MDM2-E2-Ub complex	1.559	70.75	95993	4694	99.803	0.136	0.1335	0.15	0.1848	0.2	20.479

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]
0.232	0.116		0.232		-0.752

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.614
r_dihedral_angle_4_deg	16.235
r_dihedral_angle_3_deg	12.743
r_rigid_bond_restr	7.877
r_dihedral_angle_1_deg	6.655
r_lrange_other	5.478
r_lrange_it	5.476
r_scangle_it	5.266
r_scangle_other	5.265
r_scbond_other	4.627
r_scbond_it	4.626
r_mcangle_it	3.615
r_mcangle_other	3.615
r_mcbond_other	2.989
r_mcbond_it	2.988
r_angle_refined_deg	1.773
r_angle_other_deg	1.692
r_nbd_refined	0.233
r_nbd_other	0.223
r_symmetry_nbd_other	0.211
r_symmetry_nbd_refined	0.2
r_xyhbond_nbd_refined	0.173
r_nbtor_refined	0.171
r_symmetry_xyhbond_nbd_refined	0.168
r_ncsr_local_group_2	0.12
r_chiral_restr	0.098
r_ncsr_local_group_3	0.081
r_symmetry_nbtor_other	0.078
r_ncsr_local_group_1	0.078
r_metal_ion_refined	0.024
r_bond_other_d	0.017
r_bond_refined_d	0.015
r_gen_planes_other	0.012
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4513
Nucleic Acid Atoms
Solvent Atoms	662
Heterogen Atoms	25

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing