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Flavocytochrome c3 with mesaconate bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QJD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 TrisHCl, mesaconate, NaCl, PEG8000, pH 7.8-8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.56 51.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.449 α = 90 b = 91.687 β = 91.13 c = 78.287 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 4 2003-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.1 0.975 SRS PX14.1
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 1.5 24 97.2 0.048 21 102486 99564 14.247
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) 1.5 1.55 94 0.373 3.12 9590
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 1QJD 1.5 24 94583 4978 97.21 0.15248 0.15084 0.1527 0.18353 0.1847 RANDOM 14.247
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] 0.89 -0.12 0.2 -1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.117 r_scangle_it 3.429 r_scbond_it 2.183 r_angle_refined_deg 1.511 r_mcangle_it 1.344 r_angle_other_deg 0.968 r_mcbond_it 0.796 r_nbd_refined 0.28 r_nbd_other 0.257 r_symmetry_vdw_other 0.256
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.117 r_scangle_it 3.429 r_scbond_it 2.183 r_angle_refined_deg 1.511 r_mcangle_it 1.344 r_angle_other_deg 0.968 r_mcbond_it 0.796 r_nbd_refined 0.28 r_nbd_other 0.257 r_symmetry_vdw_other 0.256 r_symmetry_hbond_refined 0.191 r_symmetry_vdw_refined 0.19 r_xyhbond_nbd_refined 0.169 r_chiral_restr 0.137 r_nbtor_other 0.084 r_metal_ion_refined 0.053 r_bond_refined_d 0.015 r_gen_planes_other 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4217 Nucleic Acid Atoms Solvent Atoms 1249 Heterogen Atoms 235
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling