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Crystal Structure of the double mutant D44A D45A Plastocyanin from Phormidium laminosum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q5B PDB entry 2Q5B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 30% PEG 8000, 0.1 M Sodium cacodylate, 0.2 M Sodium acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.94 36.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.322 α = 90 b = 33.778 β = 90 c = 78.026 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 ADSC QUANTUM 315 2007-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97 APS 19-ID
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 50 94.2 0.088 7.96 4 13923 13923 13.1
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) 1.5 1.55 96.4 0.63 2.1 3.7 1381
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 PDB entry 2Q5B 1.5 10 13102 704 94.25 0.18761 0.18468 0.183 0.2446 0.2381 RANDOM 15.917
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] 0.38 -0.15 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.716 r_dihedral_angle_3_deg 11.28 r_dihedral_angle_1_deg 5.695 r_scangle_it 3.054 r_dihedral_angle_4_deg 2.648 r_sphericity_free 2.539 r_scbond_it 2.224 r_sphericity_bonded 1.934 r_rigid_bond_restr 1.617 r_mcangle_it 1.605
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.716 r_dihedral_angle_3_deg 11.28 r_dihedral_angle_1_deg 5.695 r_scangle_it 3.054 r_dihedral_angle_4_deg 2.648 r_sphericity_free 2.539 r_scbond_it 2.224 r_sphericity_bonded 1.934 r_rigid_bond_restr 1.617 r_mcangle_it 1.605 r_angle_refined_deg 1.348 r_mcbond_it 1.081 r_nbtor_refined 0.314 r_nbd_refined 0.217 r_symmetry_vdw_refined 0.125 r_xyhbond_nbd_refined 0.123 r_symmetry_hbond_refined 0.098 r_chiral_restr 0.09 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 804 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling PHASER phasing WARP model building ARP model building