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Crystal structure of human S100A13 in the Ca2+-bound state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XK4 PDB ENTRY 1XK4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 22% PEG 3350, 0.1M HEPES-NaOH (pH 7.5), 0.2M NaCl, 1.5% 1,2,3-heptanetriol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.99 38.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.774 α = 90 b = 59.287 β = 90 c = 77.624 γ = 90
Symmetry Space Group P 21 21 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 315 Rotated-inclined double-crystal monochromator, rhodium-coated horizontal mirror 2006-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.8 50 99.1 0.066 31.5 6.9 17786 3.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.86 93 0.335 3.4 6.3
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 1XK4 1.8 47.14 16683 897 99.17 0.19732 0.19541 0.1949 0.23418 0.2316 RANDOM 24.001
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.698 r_dihedral_angle_4_deg 15.278 r_dihedral_angle_3_deg 12.271 r_dihedral_angle_1_deg 5.232 r_scangle_it 2.993 r_scbond_it 2.064 r_angle_refined_deg 1.467 r_mcangle_it 1.146 r_mcbond_it 0.859 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.698 r_dihedral_angle_4_deg 15.278 r_dihedral_angle_3_deg 12.271 r_dihedral_angle_1_deg 5.232 r_scangle_it 2.993 r_scbond_it 2.064 r_angle_refined_deg 1.467 r_mcangle_it 1.146 r_mcbond_it 0.859 r_nbtor_refined 0.308 r_nbd_refined 0.214 r_symmetry_hbond_refined 0.213 r_symmetry_vdw_refined 0.152 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.114 r_metal_ion_refined 0.083 r_bond_refined_d 0.018 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 1383 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement BSS data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing