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Crystal structure of MBL collagen-like peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3POD PDB ENTRY 3POD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 1.6M Ammonium Sulphate, 100mM MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.82 32.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.27 α = 90 b = 23.65 β = 94.09 c = 26.94 γ = 90
Symmetry Space Group C 1 2 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 focusing mirrors 2010-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.872600 ESRF ID23-2
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 1.5 23.485 99.4 0.093 4 2.9 8744
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 1.58 99.4 0.359 2 2.8 3561
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 (All) 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 3POD 1.5 21.26 8296 415 98.97 0.14344 0.14344 0.14097 0.1413 0.18981 0.1945 RANDOM 9.64
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] -0.14 0.03 0.38 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 31.194 r_scangle_it 7.113 r_dihedral_angle_1_deg 6.693 r_scbond_it 5.084 r_mcangle_it 3.345 r_angle_refined_deg 2.777 r_mcbond_it 2.323 r_rigid_bond_restr 2.192 r_angle_other_deg 1.205 r_mcbond_other 0.899
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 31.194 r_scangle_it 7.113 r_dihedral_angle_1_deg 6.693 r_scbond_it 5.084 r_mcangle_it 3.345 r_angle_refined_deg 2.777 r_mcbond_it 2.323 r_rigid_bond_restr 2.192 r_angle_other_deg 1.205 r_mcbond_other 0.899 r_chiral_restr 0.153 r_bond_refined_d 0.026 r_bond_other_d 0.016 r_gen_planes_refined 0.012 r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 515 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms
Software Software Software Name Purpose MxCuBE data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling