2ION

Crystal structure of the C-terminal MA3 domain of Pdcd4 (mouse); form2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2IOL	PDB ENTRY 2IOL, Chain A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	293	0.17 M ammonium sulfate, 0.085 M sodium acetate, 25.5% (w/v) PEG 2000 MME, 15% (v/v) glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.536	α = 90
b = 61.536	β = 90
c = 78.066	γ = 120

Symmetry
Space Group	P 31 2 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	IMAGE PLATE	MAR scanner 345 mm plate			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.57	30	99.6	0.08	20.6	5.1	24343	23715	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.571	1.612	95.45		0.501	3.2	4.6	1605

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2IOL, Chain A	1.57	30	24343	23008	1241	99.56	0.183	0.1615	0.15974	0.1948	RANDOM	15.253

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]
0.52	0.26		0.52		-0.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.605
r_dihedral_angle_4_deg	23.201
r_dihedral_angle_3_deg	11.118
r_scangle_it	4.587
r_dihedral_angle_1_deg	4.346
r_scbond_it	3.002
r_mcangle_it	1.889
r_angle_refined_deg	1.78
r_mcbond_it	1.591
r_angle_other_deg	0.968
r_mcbond_other	0.381
r_symmetry_hbond_refined	0.322
r_nbd_refined	0.252
r_symmetry_vdw_other	0.244
r_xyhbond_nbd_refined	0.218
r_nbtor_refined	0.185
r_nbd_other	0.175
r_symmetry_vdw_refined	0.174
r_chiral_restr	0.105
r_nbtor_other	0.084
r_bond_refined_d	0.022
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1036
Nucleic Acid Atoms
Solvent Atoms	185
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing