3VBG

Structure of hDM2 with Dimer Inducing Indolyl Hydantoin RO-2443

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RV1	pdb entry 1RV1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	54% saturated ammonium sulfate, 0.1M Tris, 5% PEG 550 mme, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
4.98	75.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.392	α = 90
b = 64.392	β = 90
c = 167.587	γ = 120

Symmetry
Space Group	P 32

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		2009-10-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F		APS	21-ID-F

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	2.8	30	99.5	0.053	13	3.9		19100

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	2.8	2.9	98.9		0.442	1.5	3.9	1897

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	pdb entry 1RV1	2.8	30	18025	992	99.3	0.18416	0.1822	0.21989	RANDOM	106.497

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]
-67.84			-67.84		135.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.754
r_dihedral_angle_3_deg	25.025
r_dihedral_angle_4_deg	18.807
r_dihedral_angle_1_deg	9.334
r_angle_refined_deg	2.808
r_chiral_restr	0.149
r_bond_refined_d	0.019
r_gen_planes_refined	0.011
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2810
Nucleic Acid Atoms
Solvent Atoms	19
Heterogen Atoms	112

Software

Software
Software Name	Purpose
REFMAC	refinement
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing