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The 1.5 Angstrom crystal structure of oxidized (CuII) poplar plastocyanin B at pH 4.0
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 4 277 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 2002-03-04 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 1.5 34.75 96.5 0.078 15.9 2.5 12884 12433 2 13.11
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 1.5 1.53 95.1 0.465 2.1 2.4 634
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 1.5 34.75 12425 11814 602 95.08 0.15325 0.15002 0.1581 0.21657 0.2223 RANDOM 14.47
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] -0.53 0.21 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.347 r_dihedral_angle_3_deg 13.047 r_dihedral_angle_1_deg 6.95 r_scangle_it 5.566 r_scbond_it 3.766 r_angle_refined_deg 2.423 r_mcangle_it 2.257 r_mcbond_it 1.673 r_nbtor_refined 0.314 r_symmetry_hbond_refined 0.235
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.347 r_dihedral_angle_3_deg 13.047 r_dihedral_angle_1_deg 6.95 r_scangle_it 5.566 r_scbond_it 3.766 r_angle_refined_deg 2.423 r_mcangle_it 2.257 r_mcbond_it 1.673 r_nbtor_refined 0.314 r_symmetry_hbond_refined 0.235 r_nbd_refined 0.232 r_xyhbond_nbd_refined 0.229 r_symmetry_vdw_refined 0.225 r_chiral_restr 0.184 r_bond_refined_d 0.029 r_gen_planes_refined 0.013 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_refined 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 118 Heterogen Atoms 12
Software Software Software Name Purpose MAR345 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling