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Crystal structure of Cu(I) Azurin with the metal-binding loop sequence "CTFPGHSALM" replaced with "CSPHQGAGM", at pH5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HX7 Cu(II) form of the protein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 29-31% PEG 4000, 100mM magnesium chloride, 100mM Sodium acetate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.25 45.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.905 α = 90 b = 65.345 β = 90 c = 97.707 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 93 IMAGE PLATE RIGAKU RAXIS IV Osmic "blue" 2006-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.542
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.547 54.317 99.8 0.053 0.053 10.2 6.7 33470 16.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.6 1.69 99 0.302 0.302 2.4 6.5 4783
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION Direct use of Oxidised structure in same crystal form THROUGHOUT Cu(II) form of the protein 1.6 54.31 33411 1667 99.66 0.14 0.14 0.138 0.184 0.1869 RANDOM 10.285
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] -0.97 0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.254 r_dihedral_angle_1_deg 11.236 r_dihedral_angle_3_deg 10.916 r_dihedral_angle_4_deg 10.045 r_sphericity_free 8.093 r_scangle_it 3.945 r_sphericity_bonded 3.336 r_scbond_it 2.966 r_mcangle_it 1.956 r_mcbond_it 1.595
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.254 r_dihedral_angle_1_deg 11.236 r_dihedral_angle_3_deg 10.916 r_dihedral_angle_4_deg 10.045 r_sphericity_free 8.093 r_scangle_it 3.945 r_sphericity_bonded 3.336 r_scbond_it 2.966 r_mcangle_it 1.956 r_mcbond_it 1.595 r_angle_refined_deg 1.543 r_rigid_bond_restr 1.448 r_angle_other_deg 0.925 r_mcbond_other 0.577 r_symmetry_vdw_other 0.22 r_nbd_refined 0.202 r_nbd_other 0.191 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.144 r_symmetry_hbond_refined 0.131 r_symmetry_vdw_refined 0.115 r_chiral_restr 0.102 r_nbtor_other 0.087 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_metal_ion_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1902 Nucleic Acid Atoms Solvent Atoms 448 Heterogen Atoms 2
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection MOSFLM data reduction CCP4 data scaling