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High Resolution Crystal Structure of the EGF domain of Spitz
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JL9 PDB ENTRY 1JL9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 294 15mM ammonium sulphate, 0.1M MES pH 6.5, 24% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 294K, pH 6.50
Crystal Properties Matthews coefficient Solvent content 2.17 43.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.305 α = 90 b = 36.154 β = 103.09 c = 25.362 γ = 90
Symmetry Space Group C 1 2 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 MARMOSAIC 300 mm CCD 3.0 UNDULATOR 2007-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D APS 23-ID-D
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 1.499 50 91.6 0.047 16.3 5.3 7284 -3 20.6
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) 1.499 1.55 56.6 0.21 4.6 3.6
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 (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 1JL9 1.5 30.5 7634 7284 350 91.5 0.201 0.2 0.1966 0.236 0.2346 RANDOM 20.66
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] -0.45 -0.92 0.96 -0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.263 r_dihedral_angle_3_deg 13.785 r_dihedral_angle_4_deg 11.741 r_dihedral_angle_1_deg 6.683 r_scangle_it 3.222 r_scbond_it 2.152 r_mcangle_it 1.535 r_angle_refined_deg 1.165 r_mcbond_it 1.083 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.263 r_dihedral_angle_3_deg 13.785 r_dihedral_angle_4_deg 11.741 r_dihedral_angle_1_deg 6.683 r_scangle_it 3.222 r_scbond_it 2.152 r_mcangle_it 1.535 r_angle_refined_deg 1.165 r_mcbond_it 1.083 r_nbtor_refined 0.313 r_nbd_refined 0.199 r_symmetry_hbond_refined 0.169 r_symmetry_vdw_refined 0.162 r_xyhbond_nbd_refined 0.115 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 406 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing