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MetHemoglobin 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 6SVA
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 2.82 56.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.53 α = 90.1 b = 63.08 β = 111.02 c = 54.69 γ = 90.09
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 2021-05-30 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) R Split (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 1.95 53.55 100 0.9903 0.075 10.6 176 25258
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.02 0.7593 0.4194 1.37
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 1.95 53.491 25215 1208 99.937 0.152 0.1497 0.1511 0.194 0.1938 RANDOM 65.937
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] 0.612 1.85 -1.834 -0.154
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.53 r_dihedral_angle_3_deg 14.202 r_dihedral_angle_2_deg 12.688 r_lrange_it 12.289 r_scangle_it 11.004 r_scbond_it 7.766 r_mcangle_it 6.347 r_dihedral_angle_1_deg 5.636 r_mcbond_it 5.059 r_angle_refined_deg 1.953
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.53 r_dihedral_angle_3_deg 14.202 r_dihedral_angle_2_deg 12.688 r_lrange_it 12.289 r_scangle_it 11.004 r_scbond_it 7.766 r_mcangle_it 6.347 r_dihedral_angle_1_deg 5.636 r_mcbond_it 5.059 r_angle_refined_deg 1.953 r_nbtor_refined 0.302 r_nbd_refined 0.2 r_symmetry_nbd_refined 0.15 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.088 r_symmetry_xyhbond_nbd_refined 0.084 r_bond_refined_d 0.015 r_gen_planes_refined 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2184 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling PHASER phasing