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Crystal structure of the human CLP-36 (PDLIM1) bound to the C-terminal peptide of human alpha-actinin-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other in-house model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 40% PEG 300, 0.2M Calcium acetate, 0.1M Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.74 55.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.74 α = 90 b = 38.74 β = 90 c = 246.46 γ = 120
Symmetry Space Group P 65 2 2
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 MARMOSAIC 225 mm CCD 2007-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.79987 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 50 98.3 0.114 14.3 13.8 18632 18632 18.3
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 1.59 89.6 0.55 2.8 6.6 2617
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT in-house model 1.5 41.06 18632 18632 960 98.84 0.213 0.213 0.212 0.231 0.246 RANDOM 7.375
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] 0.17 0.09 0.17 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.057 r_dihedral_angle_4_deg 9.39 r_dihedral_angle_3_deg 9.282 r_dihedral_angle_1_deg 5.118 r_scangle_it 1.082 r_angle_refined_deg 0.919 r_angle_other_deg 0.767 r_scbond_it 0.696 r_mcangle_it 0.39 r_mcbond_it 0.236
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.057 r_dihedral_angle_4_deg 9.39 r_dihedral_angle_3_deg 9.282 r_dihedral_angle_1_deg 5.118 r_scangle_it 1.082 r_angle_refined_deg 0.919 r_angle_other_deg 0.767 r_scbond_it 0.696 r_mcangle_it 0.39 r_mcbond_it 0.236 r_symmetry_vdw_other 0.213 r_nbd_refined 0.179 r_nbd_other 0.174 r_symmetry_vdw_refined 0.169 r_nbtor_refined 0.151 r_xyhbond_nbd_refined 0.107 r_metal_ion_refined 0.104 r_nbtor_other 0.074 r_symmetry_hbond_refined 0.073 r_chiral_restr 0.055 r_symmetry_metal_ion_refined 0.054 r_mcbond_other 0.048 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 677 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 26
Software Software Software Name Purpose PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection XDS data reduction XDS data scaling