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X-ray Free Electron Laser Structure of Cytochrome C Peroxidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3M23
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 10UL (350-400UM PROTEIN), 22% MPD,
50MM TRIS PHOSHATE BUFFER PH 6.0, VAPOR DIFFUSION, SITTING DROP,
TEMPERATURE 277.2K
Crystal Properties Matthews coefficient Solvent content 3.07 60.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.47 α = 90 b = 74.99 β = 90 c = 51.25 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 100 CCD RAYONIX MX-325 Data collected over two experiments, in Dec 2013 and June 2014 2013-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE XPP 1.306, 1.313 SLAC LCLS XPP
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.5 19.7 97.8 3.33 9.2 65592 65592
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 1.5 1.6 93.8 2 5.7
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 3M23 1.5 19.69 62310 3280 97.78 0.23518 0.23384 0.2436 0.26055 0.2697 RANDOM 5.141
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] 0.01 -0.02 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.43 r_dihedral_angle_4_deg 22.341 r_dihedral_angle_3_deg 12.69 r_dihedral_angle_1_deg 6.185 r_long_range_B_refined 3.895 r_long_range_B_other 3.276 r_angle_refined_deg 1.841 r_scangle_other 1.74 r_scbond_it 1.16 r_scbond_other 1.158
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.43 r_dihedral_angle_4_deg 22.341 r_dihedral_angle_3_deg 12.69 r_dihedral_angle_1_deg 6.185 r_long_range_B_refined 3.895 r_long_range_B_other 3.276 r_angle_refined_deg 1.841 r_scangle_other 1.74 r_scbond_it 1.16 r_scbond_other 1.158 r_angle_other_deg 1.14 r_mcangle_it 0.933 r_mcangle_other 0.933 r_mcbond_it 0.566 r_mcbond_other 0.565 r_chiral_restr 0.131 r_bond_refined_d 0.019 r_gen_planes_refined 0.013 r_gen_planes_other 0.01 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 2352 Nucleic Acid Atoms Solvent Atoms 293 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing