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The X-ray structure of human neuroglobin C120S mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MPM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 1.6 M ammonium sulfate,10% v/v 1,4-Dioxane, 0.1 M MES monohydrate pH 6.5
Crystal Properties Matthews coefficient Solvent content 1.93 36.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.009 α = 90 b = 119.94 β = 90 c = 38.857 γ = 90
Symmetry Space Group P 21 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 DECTRIS EIGER2 S 9M 2022-01-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.9792 SSRF BL02U1
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 1.5 50 98.73 0.06813 0.02429 0.997 18.9 9 63053 17.85
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 1.5 1.554 99.92 0.3732 0.1406 0.983 4.51 7.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4MPM 1.5 28.52 1.35 63016 3194 98.76 0.1561 0.1535 0.1554 0.2036 0.2044 24.06
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 24.2902 f_angle_d 1.5224 f_chiral_restr 0.0959 f_bond_d 0.0161 f_plane_restr 0.0105
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3445 Nucleic Acid Atoms Solvent Atoms 447 Heterogen Atoms 159
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing