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Crystal structure of murine neuroglobin at ambient pressure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4O4T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 1.6 M ammonium sulfate, 0.1 M MES, 10 % dioxane
Crystal Properties Matthews coefficient Solvent content 2.58 52.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.316 α = 90 b = 88.316 β = 90 c = 114.457 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 CCD MAR CCD 165 mm 2012-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE CRISTAL 0.4540 SOLEIL CRISTAL
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (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 2 45.821 98.7 0.104 0.119 0.056 10.2 4 11623 11623
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 99.7 0.479 0.479 0.256 1.5 4.1 1685
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4O4T 2 20 11058 552 98.1 0.1449 0.1431 0.1538 0.1805 0.1923 RANDOM 29.779
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] 0.12 0.06 0.12 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.755 r_dihedral_angle_4_deg 17.697 r_dihedral_angle_3_deg 15.933 r_dihedral_angle_1_deg 5.049 r_mcangle_it 4.192 r_mcbond_it 2.773 r_mcbond_other 2.773 r_angle_other_deg 2.144 r_angle_refined_deg 1.879 r_chiral_restr 0.131
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.755 r_dihedral_angle_4_deg 17.697 r_dihedral_angle_3_deg 15.933 r_dihedral_angle_1_deg 5.049 r_mcangle_it 4.192 r_mcbond_it 2.773 r_mcbond_other 2.773 r_angle_other_deg 2.144 r_angle_refined_deg 1.879 r_chiral_restr 0.131 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_gen_planes_other 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1172 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PHASER phasing DM phasing PDB_EXTRACT data extraction SCALA data scaling PHASER phasing BUCCANEER phasing