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Crystal Structure of Cytochrome c' from Alcaligenes xylosoxidans NCIMB 11015 at pH 6.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E83
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 6 293 12 % PEG4000, 100 mM potassium phosphate, 1 mM sodium azide
Crystal Properties Matthews coefficient Solvent content 2.71 54.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.189 α = 90 b = 53.189 β = 90 c = 181.026 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 100 CCD ADSC QUANTUM 270 2010-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0000 Photon Factory AR-NE3A
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 1.1 50 99.4 36.1 11.6 62734
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 1E83 1.11 26.31 55388 2892 95.37 0.14158 0.14053 0.1367 0.16168 0.1592 RANDOM 15.146
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] -0.06 -0.06 -0.06 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.563 r_sphericity_free 27.274 r_dihedral_angle_4_deg 24.191 r_dihedral_angle_3_deg 15.552 r_sphericity_bonded 11.523 r_rigid_bond_restr 8.517 r_dihedral_angle_1_deg 5.844 r_long_range_B_refined 3.788 r_angle_refined_deg 3.094 r_scbond_it 2.679
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.563 r_sphericity_free 27.274 r_dihedral_angle_4_deg 24.191 r_dihedral_angle_3_deg 15.552 r_sphericity_bonded 11.523 r_rigid_bond_restr 8.517 r_dihedral_angle_1_deg 5.844 r_long_range_B_refined 3.788 r_angle_refined_deg 3.094 r_scbond_it 2.679 r_mcangle_it 1.747 r_mcbond_it 1.435 r_chiral_restr 0.138 r_bond_refined_d 0.03 r_gen_planes_refined 0.029 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 949 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement