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Structure of wild-type Phormidium laminosum cytochrome c6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CTJ PDB ENTRY 1CTJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 2.5 M NACL, 100 MM IMIDAZOLE, 200 MM ZN(OAC)2, PH 6.0.
Crystal Properties Matthews coefficient Solvent content 2.2 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.364 α = 90 b = 57.364 β = 90 c = 89.553 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 CCD 2004-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 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 2 25.5 99.7 0.1 12.3 3.2 11288 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 2 2.05 100 0.23 4.8 3.1
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 1CTJ 2 25.59 10728 541 99.6 0.188 0.184 0.1875 0.255 0.2551 RANDOM 26.84
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] 0.01 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.769 r_dihedral_angle_4_deg 31.308 r_dihedral_angle_3_deg 18.321 r_dihedral_angle_1_deg 11.615 r_scangle_it 3.885 r_scbond_it 2.778 r_angle_refined_deg 1.779 r_mcangle_it 1.775 r_mcbond_it 1.053 r_symmetry_hbond_refined 0.342
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.769 r_dihedral_angle_4_deg 31.308 r_dihedral_angle_3_deg 18.321 r_dihedral_angle_1_deg 11.615 r_scangle_it 3.885 r_scbond_it 2.778 r_angle_refined_deg 1.779 r_mcangle_it 1.775 r_mcbond_it 1.053 r_symmetry_hbond_refined 0.342 r_xyhbond_nbd_refined 0.307 r_nbtor_refined 0.299 r_nbd_refined 0.29 r_symmetry_vdw_refined 0.264 r_chiral_restr 0.113 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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_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 1212 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 118
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing