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Crystal structure of heme-loaded design: HEM_3.C9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Other In house de novo designed model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 3.2M Ammonium Sulfate, 0.1M Citrate pH 5
Crystal Properties Matthews coefficient Solvent content 1.87 39.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.987 α = 90 b = 39.622 β = 90 c = 119.239 γ = 90
Symmetry Space Group P 21 21 21
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 9M 2023-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.92009 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 28.06 95.57 0.094 0.05 0.999 8.84 4.3 16611 27.26
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 88.59 1.42 0.792 0.792 1.01
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.8 28.06 0.09 16611 1650 95.57 0.1937 0.1893 0.1915 0.2318 0.2314 33.39
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 f_dihedral_angle_d 16.5229 f_angle_d 1.3951 f_chiral_restr 0.0806 f_bond_d 0.0154 f_plane_restr 0.0094
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1500 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 48
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing