7AHY

Crystal structure of Western clawed frog MDM2 RING domain homodimer

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	292	0.1 M PCTP, 25 % w/v PEG 1500

Crystal Properties
Matthews coefficient	Solvent content
2.16	42.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.559	α = 90
b = 23.76	β = 101.224
c = 55.744	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		2017-07-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97997	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	2.53	41.75	99.8	0.983	3.7	3.1		3830

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	2.53	2.6			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	7AH2	2.532	41.745	3830	198	99.532	0.22	0.2167	0.2788	42.802

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]
0.339		0.296	1.592		-1.899

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.057
r_dihedral_angle_4_deg	25.219
r_dihedral_angle_3_deg	21.365
r_lrange_it	6.951
r_lrange_other	6.948
r_dihedral_angle_1_deg	6.02
r_scangle_it	4.22
r_scangle_other	4.22
r_mcangle_it	4.195
r_mcangle_other	4.192
r_scbond_it	2.609
r_scbond_other	2.606
r_mcbond_it	2.598
r_mcbond_other	2.598
r_angle_refined_deg	1.377
r_angle_other_deg	1.226
r_symmetry_nbd_refined	0.268
r_nbd_other	0.227
r_symmetry_nbd_other	0.198
r_nbd_refined	0.183
r_nbtor_refined	0.151
r_symmetry_xyhbond_nbd_refined	0.135
r_xyhbond_nbd_refined	0.103
r_ncsr_local_group_1	0.098
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.057
r_metal_ion_refined	0.018
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	822
Nucleic Acid Atoms
Solvent Atoms	4
Heterogen Atoms	4

Software

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