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Structure of the Cytochrome c6 from the Green Alga Cladophora glomerata
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 VAPOR DIFFUSION, HANGING DROP 7.6 277 0.2 M Na-acetate, 0.1 M Na-cacodylate, pH 6.5, 30% w/v PEG 8000, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.08 40.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.063 α = 90 b = 46.063 β = 90 c = 100.526 γ = 90
Symmetry Space Group P 41 21 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 IMAGE PLATE MARRESEARCH 165-mm MAR CCD 2001-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8015 EMBL/DESY, HAMBURG X13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.3 14.8906 98.4 0.053 25.3 20.25 27067
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.3 1.32 97.6 0.311 3.6 38.68
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 (All) 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 1.3 14.684 25709 1358 98.6 0.157 0.14922 0.14339 0.148 0.19034 0.1895 RANDOM 16.595
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] 0.4835 0.4835 0.0177
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 17.8 p_staggered_tor 11.2 p_planar_tor 5.3 p_scangle_it 4.29 p_scbond_it 3.384 p_mcangle_it 2.8 p_mcbond_it 2.405 p_multtor_nbd 0.278 p_singtor_nbd 0.165 p_chiral_restr 0.138
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 17.8 p_staggered_tor 11.2 p_planar_tor 5.3 p_scangle_it 4.29 p_scbond_it 3.384 p_mcangle_it 2.8 p_mcbond_it 2.405 p_multtor_nbd 0.278 p_singtor_nbd 0.165 p_chiral_restr 0.138 p_xyhbond_nbd 0.071 p_hb_or_metal_coord 0.059 p_planar_d 0.035 p_angle_d 0.033 p_bond_d 0.024 p_plane_restr 0.016 o_bond_d_na o_bond_d_prot p_xhyhbond_nbd p_special_tor
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 674 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 43
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement