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STructure of the Discoidin I from Dictyostelium discoideum in complex with GalNAc at 1.75 angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2W94 PDB ENTRY 2W94
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 1.5 M LISO4, 100 MM NA HEPES PH 7.5, SUGAR SOAKED IN THE CRYSTAL
Crystal Properties Matthews coefficient Solvent content 2.5 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.404 α = 90 b = 274.047 β = 90 c = 86.136 γ = 90
Symmetry Space Group C 2 2 21
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 ADSC CCD 2007-09-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.75 47.4 100 0.06 8.1 4.5 86561 2
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 1.75 1.79 99.9 0.39 1.8 4.1
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 2W94 1.75 47.4 82187 4351 99.8 0.159 0.157 0.1596 0.193 0.1934 RANDOM 13.63
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] 1.08 -1.63 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.982 r_dihedral_angle_4_deg 20.299 r_dihedral_angle_3_deg 11.094 r_dihedral_angle_1_deg 7.202 r_scangle_it 3.265 r_scbond_it 2.237 r_angle_refined_deg 1.545 r_mcangle_it 1.383 r_angle_other_deg 1.146 r_mcbond_it 0.834
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.982 r_dihedral_angle_4_deg 20.299 r_dihedral_angle_3_deg 11.094 r_dihedral_angle_1_deg 7.202 r_scangle_it 3.265 r_scbond_it 2.237 r_angle_refined_deg 1.545 r_mcangle_it 1.383 r_angle_other_deg 1.146 r_mcbond_it 0.834 r_mcbond_other 0.282 r_chiral_restr 0.11 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 5975 Nucleic Acid Atoms Solvent Atoms 1053 Heterogen Atoms 140
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing