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Crystal structure of murine neuroglobin mutant F106W 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 2.6 52.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.784 α = 90 b = 88.784 β = 90 c = 114.31 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 IMAGE PLATE MAR555 FLAT PANEL mirrors 2013-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID09 0.4104 ESRF ID09
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 1.75 45.87 99.8 0.078 0.089 0.041 10.8 4.5 17681 17681 23.12
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 1.75 1.84 99.8 0.688 0.688 0.36 1 4.6 2551
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 1.75 20 16010 862 95.18 0.1554 0.1538 0.1664 0.1865 0.1999 RANDOM 30.466
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] 0.05 0.02 0.05 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.694 r_dihedral_angle_4_deg 21.716 r_dihedral_angle_3_deg 14.202 r_dihedral_angle_1_deg 4.691 r_mcangle_it 4.133 r_mcbond_it 2.7 r_mcbond_other 2.648 r_angle_other_deg 2.073 r_angle_refined_deg 1.685 r_chiral_restr 0.116
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.694 r_dihedral_angle_4_deg 21.716 r_dihedral_angle_3_deg 14.202 r_dihedral_angle_1_deg 4.691 r_mcangle_it 4.133 r_mcbond_it 2.7 r_mcbond_other 2.648 r_angle_other_deg 2.073 r_angle_refined_deg 1.685 r_chiral_restr 0.116 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_gen_planes_other 0.005 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1175 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 48
Software Software Software Name Purpose SCALA data scaling PHASER phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction