4OQ3 | pdb_00004oq3

Tetra-substituted imidazoles as a new class of inhibitors of the p53-MDM2 interaction

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4DIJ	PDB ENTRY 4DIJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	2.4M AmSO4, 0.1M Tris, 0.1M NaCitrate, pH 8.0, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.814	α = 90
b = 165.528	β = 95.06
c = 34.236	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	CCD	MARMOSAIC 225 mm CCD		2007-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.00146	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.3	20	97.8	0.119	10.9	6.1	16534	16534

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.302	2.38	97.3		0.157		2.9	1672

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 4DIJ	2.3	20	16266	16266	824	98.27	0.1959	0.1959	0.1944	0.19	0.2243	0.22	RANDOM	13.29

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]
0.68		0.26	-0.84		0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.737
r_dihedral_angle_4_deg	20.842
r_dihedral_angle_3_deg	15.9
r_dihedral_angle_1_deg	5.62
r_scangle_it	1.942
r_scbond_it	1.223
r_angle_refined_deg	1.184
r_mcangle_it	0.833
r_mcbond_it	0.496
r_nbtor_refined	0.306

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.737
r_dihedral_angle_4_deg	20.842
r_dihedral_angle_3_deg	15.9
r_dihedral_angle_1_deg	5.62
r_scangle_it	1.942
r_scbond_it	1.223
r_angle_refined_deg	1.184
r_mcangle_it	0.833
r_mcbond_it	0.496
r_nbtor_refined	0.306
r_symmetry_hbond_refined	0.204
r_nbd_refined	0.203
r_symmetry_vdw_refined	0.198
r_xyhbond_nbd_refined	0.155
r_chiral_restr	0.075
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3029
Nucleic Acid Atoms
Solvent Atoms	194
Heterogen Atoms	120

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.