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Crystal structure of the zymogen catalytic region of human MASP-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Q3X SP domain of PDB ENTRY 1Q3X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 PEG 6000, sodium chloride, TRIS/HCl buffer, pH 8.0, temperature 293K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.2 43.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.665 α = 90 b = 72.689 β = 90 c = 110.989 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 4 toroidal focusing mirror 2003-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9392 ESRF ID14-4
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 2.18 28.9 88.1 0.099 15.13 8.3 18330 18330 -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 2.18 2.25 43.1 0.575 1.9 1.9 800
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 SP domain of PDB ENTRY 1Q3X 2.18 28.9 17391 17391 938 88.18 0.20733 0.20733 0.20491 0.2109 0.25285 0.2596 RANDOM 25.915
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] -0.27 -2.56 2.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.19 r_mcangle_it 2.135 r_scangle_it 1.491 r_mcbond_it 1.29 r_scbond_it 0.988 r_angle_refined_deg 0.875 r_angle_other_deg 0.639 r_symmetry_vdw_other 0.269 r_nbd_other 0.239 r_xyhbond_nbd_refined 0.228
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.19 r_mcangle_it 2.135 r_scangle_it 1.491 r_mcbond_it 1.29 r_scbond_it 0.988 r_angle_refined_deg 0.875 r_angle_other_deg 0.639 r_symmetry_vdw_other 0.269 r_nbd_other 0.239 r_xyhbond_nbd_refined 0.228 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.168 r_symmetry_hbond_refined 0.144 r_nbtor_other 0.119 r_chiral_restr 0.056 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2909 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing