2IOS

Crystal structure of the C-terminal MA3 domain of Pdcd4 (mouse); form 3


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IOLPDB ENTRY 2IOL, chain A.

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.229310% (w/v) PEG-3000, 100 mM phosphate-citrate, 200 mM NaCl, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6152.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.254α = 90
b = 64.021β = 114.15
c = 38.453γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID0.97931APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.763099.50.03332.23.7150151485411
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.761.80695.60.2484.543.31034

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2IOL, chain A.1.7630150151418375499.480.2120.197180.194590.24853RANDOM32.106
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]
0.5-0.88-0.23-0.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.718
r_dihedral_angle_4_deg21.654
r_dihedral_angle_3_deg13.629
r_scangle_it5.534
r_dihedral_angle_1_deg5.2
r_scbond_it3.613
r_mcangle_it2.233
r_angle_refined_deg1.792
r_mcbond_it1.578
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.718
r_dihedral_angle_4_deg21.654
r_dihedral_angle_3_deg13.629
r_scangle_it5.534
r_dihedral_angle_1_deg5.2
r_scbond_it3.613
r_mcangle_it2.233
r_angle_refined_deg1.792
r_mcbond_it1.578
r_nbtor_refined0.308
r_nbd_refined0.246
r_symmetry_hbond_refined0.239
r_symmetry_vdw_refined0.231
r_xyhbond_nbd_refined0.177
r_chiral_restr0.115
r_bond_refined_d0.021
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1013
Nucleic Acid Atoms
Solvent Atoms116
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing