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Structure of human PDLIM5 in complex with the C-terminal peptide of human alpha-actinin-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PKT PDB ENTRY 2PKT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 20% PEG3350 0.20 M KSCN
Crystal Properties Matthews coefficient Solvent content 2 38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.25 α = 90 b = 36.474 β = 99.15 c = 88.706 γ = 90
Symmetry Space Group P 1 21 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 CCD MARRESEARCH MIRRORS 2007-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.5 46.4 79.7 0.04 17.2 2.69 49917
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.6 37 0.38 1.98 0.83
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2PKT 1.5 50 47380 2527 79.8 0.166 0.163 0.1718 0.215 0.1693 RANDOM 16.84
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] -0.97 -0.56 0.72 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.926 r_dihedral_angle_4_deg 21.015 r_dihedral_angle_3_deg 12.659 r_scangle_it 8.097 r_dihedral_angle_1_deg 6.81 r_scbond_it 6.178 r_mcangle_it 4.2 r_mcbond_it 3.169 r_angle_refined_deg 1.48 r_angle_other_deg 0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.926 r_dihedral_angle_4_deg 21.015 r_dihedral_angle_3_deg 12.659 r_scangle_it 8.097 r_dihedral_angle_1_deg 6.81 r_scbond_it 6.178 r_mcangle_it 4.2 r_mcbond_it 3.169 r_angle_refined_deg 1.48 r_angle_other_deg 0.93 r_symmetry_vdw_other 0.254 r_symmetry_hbond_refined 0.206 r_nbd_refined 0.204 r_nbd_other 0.194 r_symmetry_vdw_refined 0.186 r_xyhbond_nbd_refined 0.171 r_nbtor_refined 0.168 r_nbtor_other 0.086 r_chiral_restr 0.084 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 3188 Nucleic Acid Atoms Solvent Atoms 460 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing