☰ Navigation Tabs
The 5-coordinate proximal NO complex of cytochrome c prime from Shewanella frigidimarina
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YLI PDB ENTRY 2YLI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 2.2M AM SULFATE, 0.1M HEPES PH7
Crystal Properties Matthews coefficient Solvent content 2.24 45.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.3 α = 90 b = 58.279 β = 90 c = 76.137 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 PIXEL DECTRIS PILATUS 6M MIRRORS 2013-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.43 40.1 99.9 0.08 12.6 4.4 46165
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 1.43 1.51 99.9 0.77 2 4.3
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 PDB ENTRY 2YLI 1.43 46.28 43772 2339 99.8 0.16232 0.16104 0.1715 0.18631 0.193 RANDOM 15.231
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] -1.28 0.51 0.78
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 2.131 r_mcangle_it 1.865 r_scbond_it 1.823 r_mcbond_it 1.253 r_mcbond_other 1.233 r_angle_other_deg 0.897 r_chiral_restr 0.099 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 2.131 r_mcangle_it 1.865 r_scbond_it 1.823 r_mcbond_it 1.253 r_mcbond_other 1.233 r_angle_other_deg 0.897 r_chiral_restr 0.099 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1934 Nucleic Acid Atoms Solvent Atoms 305 Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing