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Crystal Structure of S100B in the Calcium and Zinc Loaded State at pH 10.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H61 pdb entry 2H61 chain A and B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 10 291 0.02 M CAPS pH 10.0, 23% PEG5000MME, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.1 41.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.75 α = 90 b = 58.18 β = 111.08 c = 47.85 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 CCD MARMOSAIC 225 mm CCD 2005-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0089 SLS X06SA
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 1.55 10 98.6 0.134 5.34 3 25152 -3 31.619
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 1.55 1.6 95.8 0.44 2
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 2H61 chain A and B 1.65 10 20791 1058 96.88 0.212 0.209 0.275 0.2466 RANDOM 18.549
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] 1.39 -0.4 0.39 -2.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.069 r_dihedral_angle_3_deg 16.433 r_dihedral_angle_4_deg 14.505 r_dihedral_angle_1_deg 5.371 r_scangle_it 4.012 r_scbond_it 2.873 r_angle_refined_deg 1.907 r_mcangle_it 1.708 r_mcbond_it 1.325 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.069 r_dihedral_angle_3_deg 16.433 r_dihedral_angle_4_deg 14.505 r_dihedral_angle_1_deg 5.371 r_scangle_it 4.012 r_scbond_it 2.873 r_angle_refined_deg 1.907 r_mcangle_it 1.708 r_mcbond_it 1.325 r_nbtor_refined 0.314 r_symmetry_hbond_refined 0.291 r_symmetry_vdw_refined 0.271 r_nbd_refined 0.246 r_xyhbond_nbd_refined 0.195 r_metal_ion_refined 0.177 r_chiral_restr 0.151 r_bond_refined_d 0.021 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1488 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 16
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction