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Crystal Structure of Cytochrome c' from Alcaligenes xylosoxidans NCIMB 11015 at pH 10.4
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 VAPOR DIFFUSION, HANGING DROP 10.4 293 24 % PEG4000, 100 mM CAPS, 50 mM magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.7 54.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.666 α = 90 b = 52.666 β = 90 c = 183.584 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 210r 2013-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 0.7500 Photon Factory AR-NW12A
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 1.48 50 99.6 64.1 20.8 26188
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 1.48 45.61 24765 1328 99.98 0.14002 0.13833 0.1374 0.17253 0.1711 RANDOM 13.352
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] -0.02 -0.02 -0.02 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.582 r_dihedral_angle_4_deg 17.942 r_dihedral_angle_3_deg 13.641 r_sphericity_bonded 7.934 r_rigid_bond_restr 7.024 r_dihedral_angle_1_deg 5.429 r_long_range_B_refined 3.436 r_mcbond_it 3.02 r_angle_refined_deg 2.77 r_scbond_it 2.595
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.582 r_dihedral_angle_4_deg 17.942 r_dihedral_angle_3_deg 13.641 r_sphericity_bonded 7.934 r_rigid_bond_restr 7.024 r_dihedral_angle_1_deg 5.429 r_long_range_B_refined 3.436 r_mcbond_it 3.02 r_angle_refined_deg 2.77 r_scbond_it 2.595 r_mcangle_it 1.923 r_chiral_restr 0.158 r_bond_refined_d 0.026 r_gen_planes_refined 0.025 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 r_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 944 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement