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Crystal Structure of S100B in the Calcium and Zinc Loaded State at pH 6.5
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, SITTING DROP 6.5 289 0.1 M MES pH 6.5 21% PEG5000MME, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.1 41.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.89 α = 90 b = 58.15 β = 111.12 c = 47.66 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 2005-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.979 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 1.5 13 97 0.077 8.54 3.9 27707 -3
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 1.5 1.6 93.4 0.517 2.3 3.5
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 2H61 chain A and B 1.5 13 26319 1386 100 0.20835 0.20559 0.2053 0.26057 0.2615 RANDOM 19.149
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] 0.08 0.07 1.19 -1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.186 r_dihedral_angle_4_deg 19.927 r_dihedral_angle_3_deg 14.792 r_dihedral_angle_1_deg 5.061 r_scangle_it 3.6 r_scbond_it 2.528 r_angle_refined_deg 1.525 r_mcangle_it 1.37 r_mcbond_it 1.019 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.186 r_dihedral_angle_4_deg 19.927 r_dihedral_angle_3_deg 14.792 r_dihedral_angle_1_deg 5.061 r_scangle_it 3.6 r_scbond_it 2.528 r_angle_refined_deg 1.525 r_mcangle_it 1.37 r_mcbond_it 1.019 r_nbtor_refined 0.311 r_metal_ion_refined 0.274 r_nbd_refined 0.224 r_symmetry_vdw_refined 0.211 r_xyhbond_nbd_refined 0.203 r_symmetry_hbond_refined 0.18 r_chiral_restr 0.107 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other 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 1440 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 19
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction