☰ Navigation Tabs
Crystal structure of human LIM protein RIL (PDLIM4) PDZ domain bound to the C-terminal peptide of human alpha-actinin-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GQ4 PDB ENTRY 1GQ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 20% PEG 10000, 0.2M MAGNESIUM CHLORIDE, 0.1M TRIS PH8.5, pH 8.50
Crystal Properties Matthews coefficient Solvent content 2.68 54.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.029 α = 90 b = 87.029 β = 90 c = 53.917 γ = 90
Symmetry Space Group P 4 21 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 MARRESEARCH 2007-01-22 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 1.9 61.55 100 0.11 18.4 9.3 16891 21.07
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 1.9 2 100 0.69 4.2 9.4
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 1GQ4 1.9 61.55 16015 853 100 0.174 0.173 0.1781 0.211 0.2148 RANDOM 19.62
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] 0.31 0.31 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.887 r_dihedral_angle_3_deg 11.624 r_dihedral_angle_4_deg 9.181 r_scangle_it 7.59 r_dihedral_angle_1_deg 6.025 r_scbond_it 5.315 r_mcangle_it 3.43 r_mcbond_it 2.476 r_angle_refined_deg 1.361 r_angle_other_deg 0.869
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.887 r_dihedral_angle_3_deg 11.624 r_dihedral_angle_4_deg 9.181 r_scangle_it 7.59 r_dihedral_angle_1_deg 6.025 r_scbond_it 5.315 r_mcangle_it 3.43 r_mcbond_it 2.476 r_angle_refined_deg 1.361 r_angle_other_deg 0.869 r_symmetry_vdw_other 0.323 r_nbd_other 0.204 r_nbd_refined 0.2 r_nbtor_refined 0.163 r_xyhbond_nbd_refined 0.139 r_symmetry_vdw_refined 0.124 r_symmetry_hbond_refined 0.124 r_nbtor_other 0.083 r_chiral_restr 0.075 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.002 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 1300 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing