7AI1 | pdb_00007ai1

Crystal structure of human MDM2-G443T RING domain homodimer bound to UbcH5B-Ub (Crystal form 2)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	292	0.1 M HEPES, 0.2 M NH4NO3, 20 % w/v PEG Smear Broad

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.267	α = 90
b = 80.687	β = 90
c = 135.909	γ = 90

Symmetry
Space Group	P 21 21 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 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	2.07	135.91	100	0.997	9	6.4		38548

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	2.07	2.11			0.584

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	2.07	69.478	38312	1887	99.517	0.215	0.2121	0.22	0.266	0.27	32.5

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]
-1.177			-0.078		1.255

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.601
r_dihedral_angle_4_deg	17.085
r_dihedral_angle_3_deg	14.648
r_dihedral_angle_1_deg	7.481
r_lrange_it	6.61
r_lrange_other	6.609
r_scangle_it	4.682
r_scangle_other	4.681
r_mcangle_it	3.794
r_mcangle_other	3.794
r_scbond_it	3.022
r_scbond_other	3.021
r_mcbond_it	2.574
r_mcbond_other	2.574
r_angle_refined_deg	1.434
r_angle_other_deg	1.26
r_symmetry_nbd_refined	0.199
r_nbd_refined	0.191
r_symmetry_nbd_other	0.186
r_symmetry_xyhbond_nbd_refined	0.186
r_nbd_other	0.168
r_xyhbond_nbd_refined	0.166
r_nbtor_refined	0.158
r_ncsr_local_group_1	0.118
r_ncsr_local_group_2	0.104
r_metal_ion_refined	0.098
r_symmetry_nbtor_other	0.09
r_ncsr_local_group_3	0.076
r_chiral_restr	0.068
r_symmetry_xyhbond_nbd_other	0.016
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4458
Nucleic Acid Atoms
Solvent Atoms	278
Heterogen Atoms	14

Software

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