3DCY

Crystal Structure a TP53-induced glycolysis and apoptosis regulator protein from Homo sapiens.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	297	PROTEIN SOLUTION (10 MG/ML SEMET PROTEIN, 0.050 M NACL, 0.0003 M TCEP, 0.005 M MES PH 6.0) MIXED IN A 1:1 RATIO WITH WELL SOLUTION (20% PEG 3350, 0.10 M MES PH 6.0) CRYOPROTECTED WITH 20% ETHYLENE GLYCOL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 297K

Crystal Properties
Matthews coefficient	Solvent content
2.1	40.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.983	α = 90
b = 76.408	β = 90
c = 79.536	γ = 90

Symmetry
Space Group	P 21 21 21

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 300 mm CCD	Adjustable focusing mirrors in K-B geometry	2008-04-04		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97942	APS	23-ID-D

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	1.748	50	99.8	0.109	16.223	13.9		25927

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)
	1.75	1.81	98.4		0.54	2.369	9.7	2514

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.748	50	25870	1313	99.511	0.182	0.18	0.229	RANDOM	21.653

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]
-0.357			0.22		0.137

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.426
r_dihedral_angle_4_deg	20.907
r_dihedral_angle_3_deg	14.257
r_dihedral_angle_1_deg	5.979
r_scangle_it	4.022
r_scbond_it	2.686
r_mcangle_it	1.696
r_angle_refined_deg	1.479
r_mcbond_it	1.079
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.426
r_dihedral_angle_4_deg	20.907
r_dihedral_angle_3_deg	14.257
r_dihedral_angle_1_deg	5.979
r_scangle_it	4.022
r_scbond_it	2.686
r_mcangle_it	1.696
r_angle_refined_deg	1.479
r_mcbond_it	1.079
r_nbtor_refined	0.304
r_nbd_refined	0.208
r_symmetry_vdw_refined	0.17
r_xyhbond_nbd_refined	0.126
r_symmetry_hbond_refined	0.118
r_chiral_restr	0.105
r_bond_refined_d	0.015
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2007
Nucleic Acid Atoms
Solvent Atoms	266
Heterogen Atoms	5

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.