7AH2 | pdb_00007ah2

Crystal structure of Zebrafish MDM2 RING domain homodimer

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VJF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	292	0.1 M imidazole, 0.12 M monosaccharides, 37.5 % (w/v) MPD_P1K_P3350 (Morpheus, Molecular Dimensions)

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.163	α = 90
b = 23.859	β = 101.664
c = 54.306	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		2017-06-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	2.872	53.185	100	0.949	6.3	3.2		2814

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	2.872	2.922			0.667

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	2VJF	2.872	45.21	2813	172	99.858	0.211	0.2065	0.21	0.2811	0.27	23.532

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]
4.54		0.157	-1.29		-3.055

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	22.676
r_dihedral_angle_3_deg	19.754
r_dihedral_angle_4_deg	18.407
r_dihedral_angle_1_deg	5.462
r_lrange_it	3.91
r_lrange_other	3.87
r_mcangle_it	2.149
r_mcangle_other	2.147
r_scangle_other	1.993
r_scangle_it	1.992
r_angle_refined_deg	1.429
r_mcbond_other	1.269
r_mcbond_it	1.268
r_scbond_it	1.241
r_scbond_other	1.24
r_angle_other_deg	1.085
r_symmetry_nbd_refined	0.205
r_symmetry_nbd_other	0.193
r_nbd_refined	0.184
r_nbd_other	0.182
r_xyhbond_nbd_refined	0.157
r_nbtor_refined	0.14
r_symmetry_xyhbond_nbd_refined	0.113
r_ncsr_local_group_1	0.104
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.052
r_metal_ion_refined	0.046
r_bond_refined_d	0.006
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	868
Nucleic Acid Atoms
Solvent Atoms	12
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing