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Crystal structure of murine neuroglobin mutant V101F 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 52.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.024 α = 90 b = 89.024 β = 90 c = 113.879 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 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 1.998 44.512 97.7 0.129 0.142 0.058 9.4 5.3 11681 11681 23
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 97.9 0.872 0.872 0.387 0.8 5.4 1669
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 10573 519 92.6 0.1578 0.1552 0.1661 0.209 0.2229 RANDOM 31.329
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] 0.13 0.06 0.13 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.738 r_dihedral_angle_4_deg 19.98 r_dihedral_angle_3_deg 15.449 r_dihedral_angle_1_deg 5.534 r_mcangle_it 4.543 r_mcbond_it 3.039 r_mcbond_other 3.031 r_angle_other_deg 2.452 r_angle_refined_deg 1.972 r_chiral_restr 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.738 r_dihedral_angle_4_deg 19.98 r_dihedral_angle_3_deg 15.449 r_dihedral_angle_1_deg 5.534 r_mcangle_it 4.543 r_mcbond_it 3.039 r_mcbond_other 3.031 r_angle_other_deg 2.452 r_angle_refined_deg 1.972 r_chiral_restr 0.15 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 r_gen_planes_other 0.008 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1176 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 XDS data reduction