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Dimeric Aquifex aeolicus cytochrome c555
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZXY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.2M ammonium sulfate, 0.1M Sodium cacodylate trihydrate, 30% PEG8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.52 51.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.591 α = 90 b = 54.464 β = 114.47 c = 65.403 γ = 90
Symmetry Space Group P 1 21 1
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 315 2013-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.6 50 98.7 0.055 0.055 24.794 3.7 50358 47953 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.66 97.8 0.599 0.599 2.019 3.7
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 2ZXY 1.6 33.121 45455 2424 98.33 0.15378 0.15049 0.1576 0.21377 0.2213 RANDOM 25.021
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] 1.25 0.1 -1.46 0.09
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 43.276 r_dihedral_angle_2_deg 32.972 r_sphericity_bonded 19.497 r_dihedral_angle_3_deg 13.237 r_long_range_B_refined 5.465 r_dihedral_angle_1_deg 5.138 r_mcangle_it 3.636 r_scbond_it 3.619 r_mcbond_it 3.016 r_mcbond_other 3.015
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 43.276 r_dihedral_angle_2_deg 32.972 r_sphericity_bonded 19.497 r_dihedral_angle_3_deg 13.237 r_long_range_B_refined 5.465 r_dihedral_angle_1_deg 5.138 r_mcangle_it 3.636 r_scbond_it 3.619 r_mcbond_it 3.016 r_mcbond_other 3.015 r_rigid_bond_restr 2.508 r_angle_refined_deg 1.489 r_angle_other_deg 0.791 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2592 Nucleic Acid Atoms Solvent Atoms 469 Heterogen Atoms 172
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling