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Crystal structure of human calprotectin(S100A8/S100A9)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MR8 1MR8 and 1IRJ experimental model PDB 1IRJ 1MR8 and 1IRJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 285 32% MPD, 0.1M Citrate (pH= 4.2), 20mM Tris (pH= 8.0), 2mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties Matthews coefficient Solvent content 2.4 47.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.509 α = 90 b = 78.697 β = 94.94 c = 177.411 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 MARRESEARCH 2003-11-15 M SINGLE WAVELENGTH 2 1 100 IMAGE PLATE MARRESEARCH 2004-07-28
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.97960 SLS X06SA 2 SYNCHROTRON BESSY BEAMLINE 14.2 0.92000 BESSY 14.2
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 1.8 30 81.03 0.119 3.8005 6.2 102635 99507 6 6
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 1.8 1.9 69.88 0.48 1.44 6.1 12460
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1MR8 and 1IRJ 1.8 30 -3 99802 94798 5004 81.02 0.1602 0.15781 0.1598 0.20475 RANDOM 27.208
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] 2.25 -1.05 -1.59 -0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.494 r_dihedral_angle_3_deg 16.05 r_dihedral_angle_4_deg 14.033 r_dihedral_angle_1_deg 5.481 r_scangle_it 3.808 r_mcangle_it 2.93 r_scbond_it 2.494 r_mcbond_it 2.05 r_angle_refined_deg 1.458 r_symmetry_vdw_refined 0.372
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.494 r_dihedral_angle_3_deg 16.05 r_dihedral_angle_4_deg 14.033 r_dihedral_angle_1_deg 5.481 r_scangle_it 3.808 r_mcangle_it 2.93 r_scbond_it 2.494 r_mcbond_it 2.05 r_angle_refined_deg 1.458 r_symmetry_vdw_refined 0.372 r_nbtor_refined 0.315 r_xyhbond_nbd_refined 0.255 r_symmetry_hbond_refined 0.254 r_nbd_refined 0.225 r_metal_ion_refined 0.118 r_chiral_restr 0.115 r_bond_refined_d 0.012 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8880 Nucleic Acid Atoms Solvent Atoms 1059 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling PHASER phasing