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Crystal structure of cytochrome c6C L50Q mutant from Synechococcus sp. PCC 7002
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EIE PDB ENTRY 4EIE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 292 Protein solution: 15 mg/ml cytochrome c6C in 0.1 M TRIS pH 7.5, 0.2 M NaCl and 1 mM PMSF; Precipitant solution: 2 M NaCl and 2 M NH4)2SO4., VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.11 41.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.38 α = 90 b = 56.38 β = 90 c = 50.05 γ = 90
Symmetry Space Group P 4 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 CCD MAR CCD 165 mm mirrors 2011-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8123 EMBL/DESY, HAMBURG X13
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 1.04 31.18 99.2 0.073 22.25 10.4 39071 39071 -3 10.127
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 1.04 1.1 98.7 0.244 7.8 7.6 5898
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 4EIE 1.04 31.18 39071 39071 977 100 0.1197 0.1197 0.1191 0.1273 0.1449 0.1524 RANDOM 10.5564
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] -0.16 -0.16 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.611 r_dihedral_angle_3_deg 11.346 r_dihedral_angle_4_deg 7.01 r_dihedral_angle_1_deg 5.941 r_scangle_it 4.466 r_scbond_it 3.269 r_mcangle_it 2.52 r_angle_refined_deg 1.855 r_mcbond_it 1.745 r_angle_other_deg 1.397
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.611 r_dihedral_angle_3_deg 11.346 r_dihedral_angle_4_deg 7.01 r_dihedral_angle_1_deg 5.941 r_scangle_it 4.466 r_scbond_it 3.269 r_mcangle_it 2.52 r_angle_refined_deg 1.855 r_mcbond_it 1.745 r_angle_other_deg 1.397 r_rigid_bond_restr 1.25 r_mcbond_other 0.584 r_chiral_restr 0.136 r_bond_refined_d 0.019 r_gen_planes_refined 0.014 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 622 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 50
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction DNA data collection XDS data reduction XDS data scaling