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High resolution structure of Plastocyanin from Phormidium laminosum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BAW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 0.1 M NA CACODYLATE BUFFER (PH 6), 0.2 M ZN ACETATE, 15% PEG 8000 , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.34 47.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.329 α = 90 b = 84.329 β = 90 c = 90.536 γ = 90
Symmetry Space Group P 43 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 ADSC QUANTUM 210 2006-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.0 ALS 8.2.1
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 1.45 42.11 99.6 0.071 25.4 9.6 57906 57906 16.8
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 1.45 1.5 96 0.626 2 3.2
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 1BAW 1.45 9.99 54607 2920 99.37 0.19075 0.18972 0.1885 0.21017 0.2082 RANDOM 17.719
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] -0.3 -0.3 0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.231 r_dihedral_angle_4_deg 18.742 r_dihedral_angle_3_deg 11.502 r_dihedral_angle_1_deg 5.974 r_scangle_it 3.124 r_sphericity_free 2.739 r_scbond_it 2.207 r_sphericity_bonded 2.138 r_rigid_bond_restr 1.723 r_mcangle_it 1.486
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.231 r_dihedral_angle_4_deg 18.742 r_dihedral_angle_3_deg 11.502 r_dihedral_angle_1_deg 5.974 r_scangle_it 3.124 r_sphericity_free 2.739 r_scbond_it 2.207 r_sphericity_bonded 2.138 r_rigid_bond_restr 1.723 r_mcangle_it 1.486 r_angle_refined_deg 1.285 r_mcbond_it 0.867 r_symmetry_hbond_refined 0.775 r_nbtor_refined 0.31 r_nbd_refined 0.262 r_xyhbond_nbd_refined 0.235 r_symmetry_vdw_refined 0.211 r_chiral_restr 0.085 r_metal_ion_refined 0.06 r_symmetry_metal_ion_refined 0.044 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2415 Nucleic Acid Atoms Solvent Atoms 268 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing