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Crystal structure of murine neuroglobin at 310 MPa 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 2.5 50.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.372 α = 90 b = 87.372 β = 90 c = 113.284 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 2.05 45.345 97.6 0.112 0.126 0.057 9.8 5 10340 10340
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 2.05 2.16 97.8 0.541 0.541 0.268 1.3 5 1509
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 2.05 20 9463 477 93.13 0.1746 0.1716 0.1782 0.2371 0.2335 RANDOM 33.088
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] -0.04 -0.02 -0.04 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.825 r_dihedral_angle_4_deg 21.628 r_dihedral_angle_3_deg 15.984 r_dihedral_angle_1_deg 6.713 r_mcangle_it 5.709 r_mcbond_it 3.93 r_mcbond_other 3.92 r_angle_refined_deg 2.219 r_angle_other_deg 2.014 r_chiral_restr 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.825 r_dihedral_angle_4_deg 21.628 r_dihedral_angle_3_deg 15.984 r_dihedral_angle_1_deg 6.713 r_mcangle_it 5.709 r_mcbond_it 3.93 r_mcbond_other 3.92 r_angle_refined_deg 2.219 r_angle_other_deg 2.014 r_chiral_restr 0.17 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 r_gen_planes_other 0.005 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1172 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PHASER phasing DM phasing PDB_EXTRACT data extraction XDS data reduction