2V1W

Crystal structure of human LIM protein RIL (PDLIM4) PDZ domain bound to the C-terminal peptide of human alpha-actinin-1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GQ4PDB ENTRY 1GQ4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.520% PEG 10000, 0.2M MAGNESIUM CHLORIDE, 0.1M TRIS PH8.5, pH 8.50
Crystal Properties
Matthews coefficientSolvent content
2.6854.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.029α = 90
b = 87.029β = 90
c = 53.917γ = 90
Symmetry
Space GroupP 4 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2007-01-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

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
11.961.551000.1118.49.31689121.07
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)
11.921000.694.29.4

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 1GQ41.961.55160158531000.1740.1730.211RANDOM19.62
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]
0.310.31-0.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.887
r_dihedral_angle_3_deg11.624
r_dihedral_angle_4_deg9.181
r_scangle_it7.59
r_dihedral_angle_1_deg6.025
r_scbond_it5.315
r_mcangle_it3.43
r_mcbond_it2.476
r_angle_refined_deg1.361
r_angle_other_deg0.869
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.887
r_dihedral_angle_3_deg11.624
r_dihedral_angle_4_deg9.181
r_scangle_it7.59
r_dihedral_angle_1_deg6.025
r_scbond_it5.315
r_mcangle_it3.43
r_mcbond_it2.476
r_angle_refined_deg1.361
r_angle_other_deg0.869
r_symmetry_vdw_other0.323
r_nbd_other0.204
r_nbd_refined0.2
r_nbtor_refined0.163
r_xyhbond_nbd_refined0.139
r_symmetry_vdw_refined0.124
r_symmetry_hbond_refined0.124
r_nbtor_other0.083
r_chiral_restr0.075
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1300
Nucleic Acid Atoms
Solvent Atoms145
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing