7C3Q | pdb_00007c3q

Human MdmX protein in complex with Nutlin3a

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6Q9W	6Q9W, 6V4F
experimental model	PDB	6V4F	6Q9W, 6V4F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	0.1 M HEPES sodium salt pH 7.5, 1.6 M Ammonium sulfate, 2%(w/v) PEG 1000

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.727	α = 90
b = 47.727	β = 90
c = 92.321	γ = 90

Symmetry
Space Group	P 43 21 2

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 EIGER X 16M		2020-01-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.979	SSRF	BL17U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.8	42.433	95.9	0.074	0.076	0.015	0.999	25.4	23		10064

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.9	92.1		0.968	1.001	0.244	0.838		15.4

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	6Q9W, 6V4F	1.801	42.433	10024	482	95.804	0.199	0.1967	0.21	0.2413	0.25	31.715

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]
0.409			0.409		-0.818

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.432
r_dihedral_angle_4_deg	16.518
r_dihedral_angle_3_deg	14.524
r_lrange_other	7.935
r_lrange_it	7.934
r_dihedral_angle_1_deg	6.42
r_scangle_it	6.381
r_scangle_other	6.376
r_scbond_it	4.092
r_mcangle_it	4.091
r_scbond_other	4.088
r_mcangle_other	4.087
r_mcbond_it	2.911
r_mcbond_other	2.895
r_angle_other_deg	2.183
r_angle_refined_deg	1.605
r_symmetry_nbd_refined	0.218
r_nbd_refined	0.213
r_symmetry_nbd_other	0.208
r_nbd_other	0.2
r_symmetry_xyhbond_nbd_refined	0.189
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.112
r_chiral_restr	0.085
r_symmetry_nbtor_other	0.081
r_bond_other_d	0.033
r_gen_planes_other	0.013
r_bond_refined_d	0.01
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	773
Nucleic Acid Atoms
Solvent Atoms	20
Heterogen Atoms	65

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction