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The 1.88 Angstrom crystal structure of oxidized (CuII) poplar plastocyanin B at pH 8.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PLC PDB ENTRY 1PLC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 2.6 M ammonium sulfate, 0.1 M sodium acetate buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.85 33.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.913 α = 90 b = 46.246 β = 90 c = 52.648 γ = 90
Symmetry Space Group P 21 21 21
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 2002-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.05 MPG/DESY, HAMBURG BW6
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 1.88 14.74 100 0.114 16.9 7 6614 6611 2 18.27
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 1.88 1.91 99.1 0.471 2.8 6.8 320
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 1PLC 1.88 14.74 6356 6258 311 98.46 0.15815 0.15391 0.1575 0.24784 0.2447 RANDOM 20.915
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] -1.77 0.17 1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.905 r_dihedral_angle_3_deg 16.612 r_dihedral_angle_1_deg 6.437 r_scangle_it 5.059 r_scbond_it 3.432 r_angle_refined_deg 2.008 r_mcangle_it 1.931 r_mcbond_it 1.269 r_nbtor_refined 0.316 r_nbd_refined 0.233
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.905 r_dihedral_angle_3_deg 16.612 r_dihedral_angle_1_deg 6.437 r_scangle_it 5.059 r_scbond_it 3.432 r_angle_refined_deg 2.008 r_mcangle_it 1.931 r_mcbond_it 1.269 r_nbtor_refined 0.316 r_nbd_refined 0.233 r_symmetry_vdw_refined 0.222 r_xyhbond_nbd_refined 0.207 r_symmetry_hbond_refined 0.171 r_chiral_restr 0.132 r_metal_ion_refined 0.027 r_bond_refined_d 0.023 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 737 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 12
Software Software Software Name Purpose MAR345 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling