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The 1.00 Angstrom crystal structure of oxidized (CuII) poplar plastocyanin A at pH 6.0
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 6 277 2.6 M ammonium sulfate, 0.1 M sodium phosphate buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.83 32.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.012 α = 90 b = 46.354 β = 90 c = 57.091 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 2002-02-21 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 15.99 96.9 0.045 19.2 3.5 42481 41152 2 5.84
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 1.02 80.7 0.26 3.5 2.9 2042
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1PLC 1 15.99 40686 39319 2096 96.64 0.12221 0.12109 0.14397 0.1503 RANDOM 10.265
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] 0.06 -0.01 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.2 r_sphericity_free 13.637 r_dihedral_angle_3_deg 10.874 r_dihedral_angle_1_deg 7.443 r_scangle_it 6.921 r_sphericity_bonded 6.534 r_scbond_it 5.203 r_mcangle_it 3.279 r_rigid_bond_restr 2.742 r_angle_refined_deg 2.663
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.2 r_sphericity_free 13.637 r_dihedral_angle_3_deg 10.874 r_dihedral_angle_1_deg 7.443 r_scangle_it 6.921 r_sphericity_bonded 6.534 r_scbond_it 5.203 r_mcangle_it 3.279 r_rigid_bond_restr 2.742 r_angle_refined_deg 2.663 r_mcbond_it 2.528 r_nbd_refined 0.573 r_xyhbond_nbd_refined 0.504 r_symmetry_hbond_refined 0.385 r_nbtor_refined 0.329 r_symmetry_vdw_refined 0.262 r_chiral_restr 0.164 r_metal_ion_refined 0.069 r_bond_refined_d 0.027 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 738 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 1
Software Software Software Name Purpose MAR345 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling