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H64A sperm whale myoglobin with a Fe-tolyl moiety
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2MBW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 9 298 100mM Tris-HCl pH 9.0, 1mM EDTA, 2.3M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.12 60.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.794 α = 90 b = 90.794 β = 90 c = 45.317 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 100 PIXEL DECTRIS PILATUS 200K mirrors 2014-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.77 50 99.9 0.07 0.074 0.025 10.1 8.6 20927
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.77 1.8 98.9 0.479 5.1
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 2MBW 1.77 39.26 19813 1067 99.64 0.1539 0.1526 0.1664 0.179 0.1846 RANDOM 21.593
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] 0.07 0.03 0.07 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.803 r_dihedral_angle_4_deg 21.318 r_sphericity_bonded 15.128 r_dihedral_angle_3_deg 14.723 r_rigid_bond_restr 9.171 r_dihedral_angle_1_deg 5.312 r_mcangle_it 2.494 r_angle_refined_deg 2.196 r_mcbond_other 1.886 r_mcbond_it 1.884
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.803 r_dihedral_angle_4_deg 21.318 r_sphericity_bonded 15.128 r_dihedral_angle_3_deg 14.723 r_rigid_bond_restr 9.171 r_dihedral_angle_1_deg 5.312 r_mcangle_it 2.494 r_angle_refined_deg 2.196 r_mcbond_other 1.886 r_mcbond_it 1.884 r_angle_other_deg 1.231 r_chiral_restr 0.202 r_bond_refined_d 0.025 r_gen_planes_refined 0.015 r_gen_planes_other 0.006 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1220 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 80
Software Software Software Name Purpose HKL-3000 phasing PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data collection HKL-3000 data reduction Aimless data scaling