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Crystal structure of Lamprey immune protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NZO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 289 1,4-Dioxane, Polyethylene glycol 20000
Crystal Properties Matthews coefficient Solvent content 3.38 63.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.049 α = 90 b = 105.049 β = 90 c = 168.08 γ = 90
Symmetry Space Group P 43 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 PIXEL PSI PILATUS 6M 2018-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.9798 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.25 89.08 99.9 28.3 16 41118
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.29
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 (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 4NZO 2.39 89.08 35701 1897 98.89 0.1953 0.1926 0.1991 0.2483 0.2504 RANDOM 52.299
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] 0.37 0.37 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.873 r_dihedral_angle_4_deg 22.485 r_dihedral_angle_3_deg 16.158 r_dihedral_angle_1_deg 7.676 r_angle_refined_deg 1.658 r_angle_other_deg 0.947 r_chiral_restr 0.1 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.873 r_dihedral_angle_4_deg 22.485 r_dihedral_angle_3_deg 16.158 r_dihedral_angle_1_deg 7.676 r_angle_refined_deg 1.658 r_angle_other_deg 0.947 r_chiral_restr 0.1 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4810 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 75
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction PHENIX phasing