3FE7 | pdb_00003fe7

Crystal Structure of HdmX bound to the p53-peptidomimetic Ac-Phe-Met-Aib-Pmp-Trp-Glu-Ac3c-Leu-NH2 at 1.35A

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GV2	PDB ENTRY 2GV2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	277	3.1M AmSo4, 1% MPD, 4% polypropyleneglycol, 0.1M MES, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.294	α = 90
b = 43.294	β = 90
c = 65.59	γ = 90

Symmetry
Space Group	P 41

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	MARRESEARCH		2007-06-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.99975	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	1.35	20	94.9	0.057	32.852	6.9		25341

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)
	1.35	1.4	61.3		0.266		1.6	1647

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	PDB ENTRY 2GV2	1.35	20	25273	1278	95.16	0.192	0.192	0.19	0.209	0.21	RANDOM	16.964

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]
-0.11			-0.11		0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.738
r_dihedral_angle_4_deg	19.477
r_dihedral_angle_3_deg	11.012
r_dihedral_angle_1_deg	6.018
r_scangle_it	3.954
r_scbond_it	2.527
r_mcangle_it	1.587
r_angle_refined_deg	1.212
r_mcbond_it	1.01
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.738
r_dihedral_angle_4_deg	19.477
r_dihedral_angle_3_deg	11.012
r_dihedral_angle_1_deg	6.018
r_scangle_it	3.954
r_scbond_it	2.527
r_mcangle_it	1.587
r_angle_refined_deg	1.212
r_mcbond_it	1.01
r_nbtor_refined	0.308
r_symmetry_hbond_refined	0.203
r_symmetry_vdw_refined	0.201
r_nbd_refined	0.195
r_xyhbond_nbd_refined	0.1
r_chiral_restr	0.089
r_bond_refined_d	0.009
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	752
Nucleic Acid Atoms
Solvent Atoms	85
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	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.