☰ Navigation Tabs
F17a-G lectin domain with bound GlcNAc(beta1-O)paranitrophenyl ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O9V PDB ENTRY 1O9V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 10% 2-propanol, 20% PEG 4000, 100mM HEPES, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.02 39.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.025 α = 90 b = 43.025 β = 90 c = 288.45 γ = 120
Symmetry Space Group P 61 2 2
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 MAR CCD 165 mm MIRRORS 2005-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 0.9183 EMBL/DESY, HAMBURG BW7A
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 1.95 50 94.4 0.075 22.2 14.7 12042 12042 19.008
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 1.95 2.02 91.6 0.297 10.2 9.7 1105
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 1O9V 1.95 48.06 11328 584 94.32 0.20587 0.20361 0.2091 0.24845 0.2496 RANDOM 17.376
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] 0.12 0.06 0.12 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.645 r_dihedral_angle_4_deg 25.027 r_dihedral_angle_3_deg 12.546 r_dihedral_angle_1_deg 6.279 r_scangle_it 2.422 r_scbond_it 1.542 r_angle_refined_deg 1.301 r_mcangle_it 1.044 r_mcbond_it 0.6 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.645 r_dihedral_angle_4_deg 25.027 r_dihedral_angle_3_deg 12.546 r_dihedral_angle_1_deg 6.279 r_scangle_it 2.422 r_scbond_it 1.542 r_angle_refined_deg 1.301 r_mcangle_it 1.044 r_mcbond_it 0.6 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1239 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 24
Software Software Software Name Purpose MAR345 data collection CNS refinement REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing