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Crystal Structure of Properdin (TSR domains N12 & 456)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 Sodium Citrate, PEG 3000
Crystal Properties Matthews coefficient Solvent content 4.44 72.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.753 α = 90 b = 114.753 β = 90 c = 232.26 γ = 90
Symmetry Space Group I 4 2 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 PIXEL DECTRIS PILATUS 6M 2016-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9763 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.516 102.881 60.5 0.185 0.196 0.063 0.996 7.5 8.8 16212 50.44
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.516 2.709 15.5 1.639 1.722 0.522 0.629 1.5 10.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.52 102.881 15443 770 60.47 0.2489 0.248 0.251 0.2672 0.27 RANDOM 64.017
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] 1.39 1.39 -2.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.341 r_dihedral_angle_3_deg 18.698 r_dihedral_angle_4_deg 15.442 r_dihedral_angle_1_deg 8.54 r_angle_refined_deg 1.731 r_angle_other_deg 1.258 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.341 r_dihedral_angle_3_deg 18.698 r_dihedral_angle_4_deg 15.442 r_dihedral_angle_1_deg 8.54 r_angle_refined_deg 1.731 r_angle_other_deg 1.258 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2705 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 190
Software Software Software Name Purpose DIALS data reduction STARANISO data scaling PHASER phasing Coot model building REFMAC refinement PDB_EXTRACT data extraction