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Crystal structure of a cyclized protein fusion of LMO4 LIM domains 1 and 2 with the LIM interacting domain of LDB1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RUT PDB ENTRY 1RUT WITH MULTIPLE CONFORMERS, SOLVENT AND ZINC ATOMS REMOVED
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 296 1M AMMONIUM SULPHATE, 0.1M TRIS, 15% GLYCEROL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.4 48.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.333 α = 90 b = 61.333 β = 90 c = 93.019 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH OSMIC MIRRORS 2005-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 1.65 50 99.4 0.034 36.3 3.9 46870 44295
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 1.65 1.69 99 0.33 2.2 2.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1RUT WITH MULTIPLE CONFORMERS, SOLVENT AND ZINC ATOMS REMOVED 1.65 10 46663 44295 2368 99.45 0.168 0.168 0.167 0.1791 0.194 0.201 RANDOM 42.98
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] -0.01 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.087 r_dihedral_angle_4_deg 16.105 r_dihedral_angle_3_deg 12.396 r_sphericity_free 9.039 r_dihedral_angle_1_deg 5.977 r_scangle_it 3.769 r_sphericity_bonded 3.594 r_scbond_it 2.831 r_rigid_bond_restr 2.204 r_mcangle_it 1.989
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.087 r_dihedral_angle_4_deg 16.105 r_dihedral_angle_3_deg 12.396 r_sphericity_free 9.039 r_dihedral_angle_1_deg 5.977 r_scangle_it 3.769 r_sphericity_bonded 3.594 r_scbond_it 2.831 r_rigid_bond_restr 2.204 r_mcangle_it 1.989 r_mcbond_it 1.755 r_angle_refined_deg 1.398 r_angle_other_deg 0.794 r_mcbond_other 0.627 r_symmetry_vdw_refined 0.207 r_nbd_refined 0.193 r_nbd_other 0.191 r_nbtor_refined 0.175 r_symmetry_vdw_other 0.159 r_symmetry_hbond_refined 0.147 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.092 r_nbtor_other 0.081 r_bond_refined_d 0.014 r_metal_ion_refined 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2420 Nucleic Acid Atoms Solvent Atoms 244 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling PHASER phasing