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Crystal structure of the MASP-1 CUB2 domain bound to Ca2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DEM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 279 24% PEG 8000, 50mM Tris buffer, pH 9.0, 20mM CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 279K
Crystal Properties Matthews coefficient Solvent content 2.16 43.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.67 α = 90 b = 36.67 β = 90 c = 168.6 γ = 90
Symmetry Space Group P 41 21 2
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 2010-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9687 Diamond I04
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 30 99.5 0.034 34.71 7.1 19395 19394
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 1.59 99.2 0.169 9.33 7.17 3037
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 3DEM 1.501 27.67 19395 18424 970 100 0.13549 0.13549 0.13328 0.1457 0.17711 0.1827 RANDOM 13.93
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] 0.02 0.02 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.239 r_dihedral_angle_4_deg 20.178 r_dihedral_angle_3_deg 13.833 r_scangle_it 7.86 r_dihedral_angle_1_deg 7.134 r_scbond_it 5.443 r_mcangle_it 3.652 r_rigid_bond_restr 2.54 r_mcbond_it 2.458 r_angle_other_deg 2.378
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.239 r_dihedral_angle_4_deg 20.178 r_dihedral_angle_3_deg 13.833 r_scangle_it 7.86 r_dihedral_angle_1_deg 7.134 r_scbond_it 5.443 r_mcangle_it 3.652 r_rigid_bond_restr 2.54 r_mcbond_it 2.458 r_angle_other_deg 2.378 r_mcbond_other 2.237 r_angle_refined_deg 2.049 r_chiral_restr 0.136 r_bond_refined_d 0.024 r_bond_other_d 0.016 r_gen_planes_refined 0.014 r_gen_planes_other 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 896 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 2
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling