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Crystal structure of Discoidin I from Dictyostelium discoideum in complex with the disaccharide GalNAc beta 1-3 galactose, at 1.6 A 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 100MM HEPES PH7.5, LI2SO4 1.2M, 20% GLYCEROL AS CRYOPROTECTANT
Crystal Properties Matthews coefficient Solvent content 2.5 50.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.58 α = 90 b = 274 β = 90 c = 85.76 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 2009-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
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 1.59 43.73 99.2 0.06 9.8 3.2 114648 2 15.1
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 1.59 1.67 99.1 0.28 2.6 3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2W94 1.59 137 108859 5754 98.97 0.15301 0.15159 0.18023 0.1948 RANDOM 10.576
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] 0.09 -0.98 0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.234 r_dihedral_angle_4_deg 20.231 r_dihedral_angle_3_deg 11.136 r_dihedral_angle_1_deg 7.095 r_scangle_it 3.451 r_scbond_it 2.275 r_angle_refined_deg 1.577 r_mcangle_it 1.475 r_angle_other_deg 0.897 r_mcbond_it 0.872
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.234 r_dihedral_angle_4_deg 20.231 r_dihedral_angle_3_deg 11.136 r_dihedral_angle_1_deg 7.095 r_scangle_it 3.451 r_scbond_it 2.275 r_angle_refined_deg 1.577 r_mcangle_it 1.475 r_angle_other_deg 0.897 r_mcbond_it 0.872 r_mcbond_other 0.277 r_chiral_restr 0.102 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.001 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 5967 Nucleic Acid Atoms Solvent Atoms 1121 Heterogen Atoms 131
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing