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DexyHemoglobin structure from serial synchrotron crystallography with fixed target
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IBE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 7.5 293.15 26%v PEG3350, 10mM HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.8 56.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.29 α = 90 b = 63.06 β = 111.01 c = 54.75 γ = 90
Symmetry Space Group C 1 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 293.15 PIXEL DECTRIS EIGER X 16M 2021-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.9762 MAX IV BioMAX
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 fixed target
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.85 53.504 100 0.9914 12.48 205 29515
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.916 0.9049 2.9
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.85 53.504 29515 1474 100 0.141 0.1396 0.1396 0.1752 0.1753 RANDOM 72.53
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] 0.469 1.67 -1.545 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.094 r_dihedral_angle_3_deg 14.816 r_lrange_it 11.961 r_dihedral_angle_2_deg 11.819 r_scangle_it 11.624 r_scbond_it 8.468 r_mcangle_it 6.571 r_dihedral_angle_1_deg 5.649 r_mcbond_it 5.283 r_angle_refined_deg 2.334
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.094 r_dihedral_angle_3_deg 14.816 r_lrange_it 11.961 r_dihedral_angle_2_deg 11.819 r_scangle_it 11.624 r_scbond_it 8.468 r_mcangle_it 6.571 r_dihedral_angle_1_deg 5.649 r_mcbond_it 5.283 r_angle_refined_deg 2.334 r_nbtor_refined 0.264 r_chiral_restr 0.175 r_nbd_refined 0.161 r_symmetry_nbd_refined 0.119 r_xyhbond_nbd_refined 0.109 r_symmetry_xyhbond_nbd_refined 0.103 r_bond_refined_d 0.014 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2190 Nucleic Acid Atoms Solvent Atoms 70 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling PHASER phasing