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X-ray structure of human Ca2+-loaded S100B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MHO pdb entry 1MHO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 289 0.1 M HEPES, 18-20%PEG400, 0.2 M CaCl2, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.06 40.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.4 α = 90 b = 81.6 β = 107 c = 71.5 γ = 90
Symmetry Space Group P 1 21 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 IMAGE PLATE MAR scanner 345 mm plate M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE SIEMENS
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 1.9 50 99 0.078 15.8 63871 2 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 1.9 2 94.1 0.315 4.9 7334
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1MHO 1.9 30.32 3.54 54870 2743 100 0.177 0.174 0.1734 0.241 0.2406 RANDOM 27.082
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] 0.29 -0.07 -0.53 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.782 r_dihedral_angle_4_deg 22.899 r_dihedral_angle_3_deg 15.47 r_dihedral_angle_1_deg 5.676 r_scangle_it 4.634 r_scbond_it 3.192 r_mcangle_it 1.73 r_angle_refined_deg 1.723 r_mcbond_it 1.484 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.782 r_dihedral_angle_4_deg 22.899 r_dihedral_angle_3_deg 15.47 r_dihedral_angle_1_deg 5.676 r_scangle_it 4.634 r_scbond_it 3.192 r_mcangle_it 1.73 r_angle_refined_deg 1.723 r_mcbond_it 1.484 r_nbtor_refined 0.311 r_symmetry_vdw_refined 0.288 r_symmetry_hbond_refined 0.251 r_nbd_refined 0.23 r_xyhbond_nbd_refined 0.216 r_metal_ion_refined 0.156 r_chiral_restr 0.125 r_bond_refined_d 0.019 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5917 Nucleic Acid Atoms Solvent Atoms 617 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data scaling CNS phasing