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Crystal structure of murine neuroglobin at 270 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 2.52 51.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.56 α = 90 b = 87.56 β = 90 c = 113.636 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 1.9 45.47 99.8 0.093 0.106 0.049 10.3 4.7 13380 13380
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 1.9 2 99.7 0.473 0.473 0.244 1.6 4.7 1908
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 1.9 20 12703 662 99.49 0.1711 0.1686 0.1766 0.2214 0.2297 RANDOM 31.738
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] 0.09 0.04 0.09 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.262 r_dihedral_angle_3_deg 16.351 r_dihedral_angle_4_deg 12.846 r_dihedral_angle_1_deg 5.778 r_mcangle_it 4.975 r_mcbond_it 3.337 r_mcbond_other 3.337 r_angle_refined_deg 2.01 r_angle_other_deg 1.975 r_chiral_restr 0.142
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.262 r_dihedral_angle_3_deg 16.351 r_dihedral_angle_4_deg 12.846 r_dihedral_angle_1_deg 5.778 r_mcangle_it 4.975 r_mcbond_it 3.337 r_mcbond_other 3.337 r_angle_refined_deg 2.01 r_angle_other_deg 1.975 r_chiral_restr 0.142 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_gen_planes_other 0.006 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1172 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PHASER phasing DM phasing PDB_EXTRACT data extraction