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Crystal structure of the first fibronectin domain of human NCAM1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UEM PDB Entry: 1UEM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.1 298 0.3 M Calcium chloride, 17% PEG 3350, 10% PEG 400 (the latter only in the drop), pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 1.9 35.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.76 α = 90 b = 53.88 β = 90 c = 74.07 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 QUANTUM 210 2005-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.9766 CHESS A1
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 1.69 30 99 0.095 12.88 7 9851 9851 -3 25.195
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) 1.69 1.79 94.4 0.487 3.1 1500
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 (All) 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: 1UEM 1.7 20 9694 9694 941 99.69 0.219 0.212 0.2113 0.286 0.2843 RANDOM 19.456
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] 0.86 -1.89 1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.43 r_dihedral_angle_3_deg 13.36 r_dihedral_angle_4_deg 11.776 r_dihedral_angle_1_deg 6.978 r_scangle_it 3.306 r_scbond_it 1.957 r_angle_refined_deg 1.286 r_mcangle_it 1.189 r_mcbond_it 0.652 r_symmetry_hbond_refined 0.345
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.43 r_dihedral_angle_3_deg 13.36 r_dihedral_angle_4_deg 11.776 r_dihedral_angle_1_deg 6.978 r_scangle_it 3.306 r_scbond_it 1.957 r_angle_refined_deg 1.286 r_mcangle_it 1.189 r_mcbond_it 0.652 r_symmetry_hbond_refined 0.345 r_symmetry_vdw_refined 0.305 r_nbtor_refined 0.296 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.202 r_chiral_restr 0.082 r_metal_ion_refined 0.054 r_bond_refined_d 0.01 r_symmetry_metal_ion_refined 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 793 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 1
Software Software Software Name Purpose XSCALE data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction XDS data scaling