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Structure of the imidazole-adduct of the Phormidium laminosum cytochrome c6 Q51V variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V08 pdb entry 2V08
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.6 291 0.4 M NaH2PO4/1.6 M K2HPO4, 0.1 M imidazole ph 8.0, 0.2 M NaCl., VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.19 43.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.616 α = 90 b = 45.616 β = 90 c = 64.707 γ = 120
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 mirrors 2006-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9794 ESRF ID29
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 1.4 25.031 97.7 0.068 18 6.1 15086 2 2
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 1.4 1.45 97 0.4 3.3 4.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 2V08 1.4 25.03 2 15086 13988 746 97.67 0.18764 0.18594 0.1917 0.22227 0.2263 RANDOM 9.884
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.776 r_dihedral_angle_4_deg 28.11 r_dihedral_angle_1_deg 13.647 r_dihedral_angle_3_deg 13.189 r_sphericity_free 3.694 r_scangle_it 2.808 r_scbond_it 2.097 r_rigid_bond_restr 1.671 r_sphericity_bonded 1.613 r_mcangle_it 1.543
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.776 r_dihedral_angle_4_deg 28.11 r_dihedral_angle_1_deg 13.647 r_dihedral_angle_3_deg 13.189 r_sphericity_free 3.694 r_scangle_it 2.808 r_scbond_it 2.097 r_rigid_bond_restr 1.671 r_sphericity_bonded 1.613 r_mcangle_it 1.543 r_angle_refined_deg 1.37 r_mcbond_it 1.186 r_xyhbond_nbd_refined 1.099 r_angle_other_deg 1.028 r_nbd_refined 0.313 r_symmetry_vdw_other 0.289 r_mcbond_other 0.289 r_symmetry_hbond_refined 0.237 r_nbd_other 0.204 r_symmetry_vdw_refined 0.184 r_nbtor_refined 0.173 r_nbtor_other 0.083 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 589 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 48
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling