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Somatic cytochrome c from Buergeria japonica frog
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 40% PEG 400, 0.1M Tris-HCl buffer (pH 8.5), 0.2M lithium sulfate, compromising with 100nL protein solution and 100nL reservoir solution
Crystal Properties Matthews coefficient Solvent content 2.073 40.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.46 α = 90 b = 72.46 β = 90 c = 35.9 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 STFC Large Pixel Detector 2024-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97627 Diamond I03
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 2.49 51.24 94.1 0.094 0.094 0.015 1 29.2 30.6 3434
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 2.49 2.53 36.9 0.464 0.643 0.443 0.341 1.4 1.4
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 2.49 36.26 3247 162 93.35 0.21606 0.21262 0.2183 0.27809 0.2646 RANDOM 41.389
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] -0.21 -0.21 0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.284 r_dihedral_angle_4_deg 24.817 r_dihedral_angle_3_deg 20.732 r_long_range_B_refined 9.201 r_long_range_B_other 9.197 r_dihedral_angle_1_deg 7.822 r_scangle_other 6.988 r_mcangle_it 5.21 r_mcangle_other 5.205 r_scbond_other 4.407
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.284 r_dihedral_angle_4_deg 24.817 r_dihedral_angle_3_deg 20.732 r_long_range_B_refined 9.201 r_long_range_B_other 9.197 r_dihedral_angle_1_deg 7.822 r_scangle_other 6.988 r_mcangle_it 5.21 r_mcangle_other 5.205 r_scbond_other 4.407 r_scbond_it 4.4 r_mcbond_it 3.332 r_mcbond_other 3.33 r_angle_refined_deg 2.455 r_angle_other_deg 1.273 r_chiral_restr 0.137 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.005 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 803 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement xia2.multiplex data reduction xia2.multiplex data scaling PHASER phasing