3REP

Crystal structure of the ILK/alpha-parvin core complex (MnATP)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3KMWPDB ENTRY 3KMW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.827750 mM Bis-Tris Propane, 12.5 (w/v) PEG 5000 MME, 5% (v/v) 1-propyl alcohol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.5952.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.022α = 90
b = 116.28β = 101.53
c = 47.284γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2011-01-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
11.843.1394.20.0345.1540605
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)
1.81.8676.20.1364.22

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 3KMW1.834.643752619840.205830.204170.23783RANDOM26.042
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]
0.140.020.19-0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.388
r_dihedral_angle_4_deg16.791
r_dihedral_angle_3_deg13.868
r_dihedral_angle_1_deg5.719
r_scangle_it3.285
r_scbond_it2.326
r_mcangle_it1.537
r_angle_refined_deg1.472
r_mcbond_it0.972
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.388
r_dihedral_angle_4_deg16.791
r_dihedral_angle_3_deg13.868
r_dihedral_angle_1_deg5.719
r_scangle_it3.285
r_scbond_it2.326
r_mcangle_it1.537
r_angle_refined_deg1.472
r_mcbond_it0.972
r_nbtor_refined0.304
r_nbd_refined0.197
r_symmetry_vdw_refined0.167
r_xyhbond_nbd_refined0.162
r_symmetry_hbond_refined0.106
r_chiral_restr0.099
r_bond_refined_d0.017
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3157
Nucleic Acid Atoms
Solvent Atoms328
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
CNSrefinement
StructureStudiodata collection
d*TREKdata reduction
d*TREKdata scaling
CNSphasing