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Marsupenaeus japonicus ferritin mutant (T158H) pH 4.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6A4U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293.15 2M NaCl, 100 mM KH2PO3/NaHPO3 pH 4.0
Crystal Properties Matthews coefficient Solvent content 3.46 64.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.435 α = 90 b = 117.435 β = 90 c = 117.435 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 273.15 PIXEL DECTRIS PILATUS3 6M 2019-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.9785 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 50 100 0.127 0.13 0.03 3.6 19.1 71219
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 1.6 1.66 100 1.031 1.06 0.245 0.844 18.6
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 6A4U 1.6 23.5 67759 3397 99.95 0.1711 0.1702 0.1835 0.1896 0.1935 RANDOM 19.296
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.366 r_dihedral_angle_4_deg 17.787 r_dihedral_angle_3_deg 13.977 r_dihedral_angle_1_deg 5.991 r_angle_refined_deg 1.651 r_angle_other_deg 1.164 r_chiral_restr 0.081 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.366 r_dihedral_angle_4_deg 17.787 r_dihedral_angle_3_deg 13.977 r_dihedral_angle_1_deg 5.991 r_angle_refined_deg 1.651 r_angle_other_deg 1.164 r_chiral_restr 0.081 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2724 Nucleic Acid Atoms Solvent Atoms 267 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction