3A5L

Crystal Structure of a Dictyostelium P109A Mg2+-Actin in Complex with Human Gelsolin Segment 1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3A5NPDB ENTRY 3A5N

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.1961.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.852α = 90
b = 69.005β = 90
c = 180.881γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-02-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.00000Photon FactoryBL-5A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.39500.0722858835
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.392.490.12313.92

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3A5N2.448.1328410143299.40.190.1890.207RANDOM37.333
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]
0.86-2.291.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.476
r_dihedral_angle_4_deg28.716
r_dihedral_angle_3_deg18.486
r_dihedral_angle_1_deg6.1
r_scangle_it5.097
r_scbond_it3.792
r_mcangle_it2.271
r_angle_refined_deg2.007
r_mcbond_it1.588
r_nbtor_refined0.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.476
r_dihedral_angle_4_deg28.716
r_dihedral_angle_3_deg18.486
r_dihedral_angle_1_deg6.1
r_scangle_it5.097
r_scbond_it3.792
r_mcangle_it2.271
r_angle_refined_deg2.007
r_mcbond_it1.588
r_nbtor_refined0.317
r_symmetry_hbond_refined0.316
r_symmetry_vdw_refined0.246
r_nbd_refined0.228
r_xyhbond_nbd_refined0.21
r_metal_ion_refined0.135
r_chiral_restr0.12
r_bond_refined_d0.018
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3790
Nucleic Acid Atoms
Solvent Atoms293
Heterogen Atoms30

Software

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