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X-ray structure of CO-bound sperm whale myoglobin using a fixed target crystallography chip
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VXA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 9 293 10 mM Tris-HCl, pH 9.0, 2.2-2.5 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.18 43.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.13 α = 90 b = 46.483 β = 90 c = 84.521 γ = 90
Symmetry Space Group P 21 21 21
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 RAYONIX MX170-HS 2015-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE XPP 1.293 SLAC LCLS XPP
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 33.43 100 0.996 6 51.6 12354
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9
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 1VXA 1.9 33.43 11780 602 99.97 0.21402 0.21169 0.2205 0.259 0.2614 RANDOM 39.726
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] 0.66 -0.34 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.573 r_dihedral_angle_4_deg 24.083 r_dihedral_angle_3_deg 16.599 r_long_range_B_refined 7.436 r_long_range_B_other 7.434 r_scangle_other 6.597 r_dihedral_angle_1_deg 5.684 r_scbond_it 4.299 r_scbond_other 4.284 r_mcangle_it 3.753
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.573 r_dihedral_angle_4_deg 24.083 r_dihedral_angle_3_deg 16.599 r_long_range_B_refined 7.436 r_long_range_B_other 7.434 r_scangle_other 6.597 r_dihedral_angle_1_deg 5.684 r_scbond_it 4.299 r_scbond_other 4.284 r_mcangle_it 3.753 r_mcangle_other 3.751 r_mcbond_it 2.931 r_mcbond_other 2.877 r_angle_refined_deg 1.704 r_angle_other_deg 0.987 r_chiral_restr 0.131 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1225 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement Cheetah data collection DIALS data scaling CPPXFEL data processing CPPXFEL data reduction CPPXFEL data scaling PHASER phasing