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H64Q 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 VAPOR DIFFUSION, HANGING DROP 7.4 293 100 mM Tris-Hcl pH7.4, 1 mM EDTA, 3.0 M Ammonium Sulfate
Crystal Properties Matthews coefficient Solvent content 1.89 35.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.261 α = 90 b = 30.334 β = 105.27 c = 64.37 γ = 90
Symmetry Space Group P 1 21 1
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 2014-04-02 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 1.88 50 99.8 0.036 0.042 0.021 16.3 3.7 10620
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 1.88 1.91 99.1 0.119 3.1
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 1.88 33 10079 528 99.3 0.1525 0.15 0.1611 0.1993 0.2055 RANDOM 20.62
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] -0.58 -1 -0.12 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.34 r_dihedral_angle_4_deg 27.103 r_sphericity_bonded 17.388 r_dihedral_angle_3_deg 14.787 r_rigid_bond_restr 6.875 r_dihedral_angle_1_deg 5.314 r_mcangle_it 2.524 r_angle_refined_deg 2.036 r_mcbond_it 1.806 r_mcbond_other 1.776
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.34 r_dihedral_angle_4_deg 27.103 r_sphericity_bonded 17.388 r_dihedral_angle_3_deg 14.787 r_rigid_bond_restr 6.875 r_dihedral_angle_1_deg 5.314 r_mcangle_it 2.524 r_angle_refined_deg 2.036 r_mcbond_it 1.806 r_mcbond_other 1.776 r_angle_other_deg 1.12 r_chiral_restr 0.136 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 r_gen_planes_other 0.004 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1202 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 71
Software Software Software Name Purpose HKL-3000 phasing PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data collection HKL-3000 data reduction