6Q9L | pdb_00006q9l

HDM2 (17-111, WILDTYPE) COMPLEXED WITH COMPOUND 9 AT 1.13A; Structural states of Hdm2 and HdmX: X-ray elucidation of adaptations and binding interactions for different chemical compound classes

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	2.7M AmSO4, 0.2M NaI, 0.2M NaCl, 0.2M TRIS

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.773	α = 90
b = 87.407	β = 90
c = 37.141	γ = 90

Symmetry
Space Group	P 21 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	CCD	MARMOSAIC 225 mm CCD		2007-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.97848	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	1.13	20	91.2	0.065	12.1	5.6		63421

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	1.13	1.17	70.5		0.178	3.05	2.3

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4DIJ	1.13	20	60546	3262	91.61	0.1788	0.1782	0.1759	0.1898	0.1882	RANDOM	11.377

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]
-0.54			-0.18		0.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.693
r_dihedral_angle_4_deg	17.987
r_dihedral_angle_3_deg	12.801
r_sphericity_free	7.067
r_sphericity_bonded	6.451
r_dihedral_angle_1_deg	5.295
r_angle_refined_deg	1.585
r_rigid_bond_restr	1.474
r_nbtor_refined	0.32
r_nbd_refined	0.212
r_symmetry_hbond_refined	0.187
r_xyhbond_nbd_refined	0.149
r_symmetry_vdw_refined	0.144
r_chiral_restr	0.097
r_bond_refined_d	0.013
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1548
Nucleic Acid Atoms
Solvent Atoms	266
Heterogen Atoms	100

Software

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