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Crystal structure of a distal-less homeobox protein 5 (Dlx5) from Homo sapiens at 1.85 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IG7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 289 0.08M sodium chloride, 45.00% 2-methyl-2,4-pentanediol, 0.012M spermine tetrahydrochloride, 0.1M sodium cacodylate pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.28 46.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.182 α = 84.13 b = 42.913 β = 77.33 c = 56.104 γ = 67.13
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 325 mm CCD Vertical focusing mirror; double crystal Si(111) monochromator 2014-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 SSRL BL14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.85 22.303 95.5 0.046 8 1.9 23348 23348 33.646
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.9 94.1 0.271 0.271 2.5 1.9 1723
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 1IG7 1.85 22.303 23315 1188 95.14 0.185 0.1829 0.1917 0.2252 0.2306 RANDOM 47.0789
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] 1.79 1.68 0.94 -3.44 -1.41 3.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.428 r_dihedral_angle_4_deg 23.005 r_dihedral_angle_3_deg 13.37 r_dihedral_angle_1_deg 4.955 r_angle_other_deg 1.409 r_angle_refined_deg 1.316 r_chiral_restr 0.1 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.428 r_dihedral_angle_4_deg 23.005 r_dihedral_angle_3_deg 13.37 r_dihedral_angle_1_deg 4.955 r_angle_other_deg 1.409 r_angle_refined_deg 1.316 r_chiral_restr 0.1 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1008 Nucleic Acid Atoms 1114 Solvent Atoms 233 Heterogen Atoms
Software Software Software Name Purpose MolProbity model building PDB_EXTRACT data extraction PHASER phasing SCALA data scaling REFMAC refinement MOSFLM data reduction