7AHZ

Crystal structure of Western clawed frog MDM2 RING domain homodimer bound to UbcH5B-Ub

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	292	0.1 M HEPES, 10 % w/v PEG 20000

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.03	α = 90
b = 153.15	β = 107.01
c = 82.08	γ = 90

Symmetry
Space Group	P 1 21 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 EIGER2 XE 16M		2017-12-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	Diamond	I03

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	1.82	52.623	98.1	0.998	13.8	3.4		113701

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	1.82	1.85			0.652

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5MNJ	1.82	52.623	113660	5516	98.025	0.197	0.1949	0.2305	48.798

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]
-0.827		-0.094	-3.237		3.472

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.461
r_dihedral_angle_4_deg	15.583
r_dihedral_angle_3_deg	14.674
r_lrange_it	9.507
r_lrange_other	9.491
r_scangle_it	7.754
r_scangle_other	7.753
r_dihedral_angle_1_deg	6.253
r_mcangle_it	5.581
r_mcangle_other	5.58
r_scbond_it	5.21
r_scbond_other	5.21
r_mcbond_other	4.201
r_mcbond_it	4.2
r_angle_refined_deg	1.462
r_angle_other_deg	1.356
r_nbd_other	0.227
r_symmetry_xyhbond_nbd_refined	0.213
r_nbd_refined	0.197
r_symmetry_nbd_other	0.191
r_symmetry_nbd_refined	0.183
r_xyhbond_nbd_refined	0.165
r_nbtor_refined	0.161
r_ncsr_local_group_13	0.116
r_ncsr_local_group_1	0.114
r_ncsr_local_group_17	0.111
r_ncsr_local_group_11	0.11
r_ncsr_local_group_4	0.106
r_ncsr_local_group_2	0.105
r_ncsr_local_group_16	0.105
r_ncsr_local_group_5	0.103
r_ncsr_local_group_10	0.103
r_ncsr_local_group_12	0.095
r_ncsr_local_group_15	0.093
r_metal_ion_refined	0.091
r_ncsr_local_group_9	0.091
r_ncsr_local_group_18	0.09
r_ncsr_local_group_3	0.088
r_ncsr_local_group_6	0.084
r_symmetry_nbtor_other	0.083
r_ncsr_local_group_14	0.073
r_chiral_restr	0.072
r_ncsr_local_group_7	0.066
r_ncsr_local_group_8	0.063
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_symmetry_xyhbond_nbd_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8781
Nucleic Acid Atoms
Solvent Atoms	356
Heterogen Atoms	9

Software

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