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Crystal structure of C35 bound to Hem
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 293 3.0 M Ammonium sulfate; 1% (w/v) MPD
Crystal Properties Matthews coefficient Solvent content 2.82 56.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.178 α = 90 b = 92.178 β = 90 c = 142.973 γ = 120
Symmetry Space Group P 32 2 1
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 EIGER2 X 16M 2023-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 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 1.51 53.255 100 0.095 0.097 0.022 1 14.5 20.1 110596
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 1.51 1.54 4.399 4.559 1.178 0.324 0.3 14.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.51 53.255 109875 5451 99.403 0.186 0.1844 0.1954 0.2149 0.2238 31.198
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] 0.63 0.315 0.63 -2.043
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.01 r_dihedral_angle_3_deg 14.686 r_dihedral_angle_2_deg 10.615 r_lrange_it 6.822 r_lrange_other 6.822 r_scangle_it 5.72 r_scangle_other 5.719 r_dihedral_angle_1_deg 5.286 r_scbond_it 4.16 r_scbond_other 4.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.01 r_dihedral_angle_3_deg 14.686 r_dihedral_angle_2_deg 10.615 r_lrange_it 6.822 r_lrange_other 6.822 r_scangle_it 5.72 r_scangle_other 5.719 r_dihedral_angle_1_deg 5.286 r_scbond_it 4.16 r_scbond_other 4.16 r_mcangle_other 2.655 r_mcangle_it 2.654 r_mcbond_it 2.311 r_mcbond_other 2.267 r_angle_refined_deg 1.555 r_angle_other_deg 0.548 r_nbd_other 0.265 r_nbd_refined 0.256 r_symmetry_nbd_refined 0.251 r_nbtor_refined 0.184 r_symmetry_nbd_other 0.182 r_xyhbond_nbd_refined 0.159 r_symmetry_xyhbond_nbd_refined 0.127 r_chiral_restr 0.08 r_symmetry_nbtor_other 0.069 r_xyhbond_nbd_other 0.057 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d 0.009 r_gen_planes_other 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4363 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms 412
Software Software Software Name Purpose REFMAC refinement xia2 data scaling xia2 data reduction PHASER phasing