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Crystal structure of the spinach plastocyanin mutants G8D/K30C/T69C and K30C/T69C- a study of the effect on crystal packing and thermostability from the introduction of a novel disulfide bond
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AG6 PDB ENTRY 1AG6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 21% PEG 3350, 0.25M MgCl2, 0.1M Na-acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.41 48.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.32 α = 90 b = 52.32 β = 90 c = 127.36 γ = 120
Symmetry Space Group P 32 2 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 MARRESEARCH 2001-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 0.991 MAX II I711
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 1.9 45.18 97.3 0.03 53.62 11.6 16181 16181 -3 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) 1.9 2.1 94.7 0.047 38.05 10.7
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 (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 1AG6 1.9 19.2 16181 15359 820 98.05 0.15925 0.15689 0.1691 0.20379 0.2119 RANDOM 13.618
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] 0.23 0.11 0.23 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.711 r_dihedral_angle_1_deg 6.101 r_scangle_it 4.722 r_scbond_it 2.86 r_mcangle_it 1.751 r_angle_refined_deg 1.624 r_mcbond_it 0.961 r_angle_other_deg 0.799 r_symmetry_vdw_refined 0.341 r_symmetry_vdw_other 0.328
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.711 r_dihedral_angle_1_deg 6.101 r_scangle_it 4.722 r_scbond_it 2.86 r_mcangle_it 1.751 r_angle_refined_deg 1.624 r_mcbond_it 0.961 r_angle_other_deg 0.799 r_symmetry_vdw_refined 0.341 r_symmetry_vdw_other 0.328 r_nbd_other 0.255 r_nbd_refined 0.193 r_symmetry_hbond_refined 0.157 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.1 r_nbtor_other 0.086 r_xyhbond_nbd_other 0.063 r_bond_refined_d 0.015 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_metal_ion_refined 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 1466 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data scaling AMoRE phasing