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Spectroscopically-validated structure of cytochrome c prime from Alcaligenes xylosoxidans, reduced by X-ray irradiation at 160K
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 7.5 AMMONIUM SULFATE, HEPES PH 7.5
Crystal Properties Matthews coefficient Solvent content 2.63 53.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.623 α = 90 b = 53.623 β = 90 c = 181.724 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 160 PIXEL DECTRIS PILATUS 6M MIRRORS 2013-03-13 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 1.77 45 98.6 0.05 11.7 4.2 15687
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 1.87 79.4 0.7 2 4.4
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 1.77 45.03 14900 785 98.09 0.20562 0.20394 0.2092 0.23885 0.2432 RANDOM 34.666
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] 0.6 0.6 0.6 -1.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.602 r_dihedral_angle_4_deg 17.617 r_dihedral_angle_3_deg 13.066 r_dihedral_angle_1_deg 4.926 r_mcangle_it 3.541 r_scbond_it 2.91 r_mcbond_it 2.566 r_mcbond_other 2.564 r_angle_refined_deg 2.073 r_angle_other_deg 0.893
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.602 r_dihedral_angle_4_deg 17.617 r_dihedral_angle_3_deg 13.066 r_dihedral_angle_1_deg 4.926 r_mcangle_it 3.541 r_scbond_it 2.91 r_mcbond_it 2.566 r_mcbond_other 2.564 r_angle_refined_deg 2.073 r_angle_other_deg 0.893 r_chiral_restr 0.095 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 949 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling