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Crystal structure of murine neuroglobin mutant V101F at 150 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 2.6 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 1.95 43.964 99.4 0.089 0.102 0.05 10.2 4.1 12433 12433 26.06
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 1.95 2.06 99.7 0.729 0.729 0.41 0.7 4.2 1807
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 10552 542 92.54 0.1552 0.1529 0.165 0.2027 0.2075 RANDOM 31.515
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 30.107 r_dihedral_angle_4_deg 18.08 r_dihedral_angle_3_deg 14.763 r_dihedral_angle_1_deg 5.729 r_mcangle_it 4.435 r_mcbond_it 2.983 r_mcbond_other 2.956 r_angle_other_deg 2.206 r_angle_refined_deg 2 r_chiral_restr 0.148
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.107 r_dihedral_angle_4_deg 18.08 r_dihedral_angle_3_deg 14.763 r_dihedral_angle_1_deg 5.729 r_mcangle_it 4.435 r_mcbond_it 2.983 r_mcbond_other 2.956 r_angle_other_deg 2.206 r_angle_refined_deg 2 r_chiral_restr 0.148 r_bond_refined_d 0.021 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 PHASER phasing DM phasing PDB_EXTRACT data extraction XDS data reduction SCALA data scaling