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Crystal Structure Analysis of Space-grown Lysozyme - Ground experiment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KXK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIQUID DIFFUSION 4.6 296 PEG 6000, NaCl, Na Acetate
Crystal Properties Matthews coefficient Solvent content 2.02 38.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.866 α = 90 b = 78.866 β = 90 c = 37.155 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 DECTRIS EIGER X 16M Flat bent collimating Rh coated mirror, toroidal focussing mirror 2019-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 1.19499 SSRL BL14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.6 55.767 96.2 0.045 0.054 0.028 10.9 3.2 15331 20.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.69 99.6 0.619 0.619 0.755 0.426 0.9 3
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 5kxk 1.6 30 14505 782 95.47 0.1727 0.17 0.1799 0.2202 0.2184 RANDOM 28.344
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] -0.46 -0.46 0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.383 r_dihedral_angle_4_deg 25.303 r_dihedral_angle_3_deg 14.841 r_dihedral_angle_1_deg 6.426 r_angle_refined_deg 1.943 r_angle_other_deg 1.185 r_chiral_restr 0.136 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.383 r_dihedral_angle_4_deg 25.303 r_dihedral_angle_3_deg 14.841 r_dihedral_angle_1_deg 6.426 r_angle_refined_deg 1.943 r_angle_other_deg 1.185 r_chiral_restr 0.136 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling EPMR phasing PDB_EXTRACT data extraction