☰ Navigation Tabs
Crystal structure of Cu(II) Azurin with the metal-binding loop sequence "CTFPGHSALM" replaced with "CSPHQGAGM"
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AZU PDB entry 4AZU, with residues 112-121 removed
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 2.26 45.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.989 α = 90 b = 65.276 β = 90 c = 97.909 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" 2006-03-08 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 1.54 54.313 96.6 0.051 0.051 9.6 4.3 36537 17.4
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) 1.54 1.62 86 0.341 0.341 2 4.1 4673
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 4AZU, with residues 112-121 removed 1.55 30 36219 1810 97.76 0.147 0.147 0.144 0.1521 0.19 0.197 RANDOM 9.984
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] -0.35 -0.28 0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.651 r_dihedral_angle_4_deg 12.939 r_dihedral_angle_3_deg 10.834 r_sphericity_free 8.084 r_dihedral_angle_1_deg 6.365 r_scangle_it 4.206 r_sphericity_bonded 3.249 r_scbond_it 3.209 r_mcangle_it 2.109 r_mcbond_it 1.698
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.651 r_dihedral_angle_4_deg 12.939 r_dihedral_angle_3_deg 10.834 r_sphericity_free 8.084 r_dihedral_angle_1_deg 6.365 r_scangle_it 4.206 r_sphericity_bonded 3.249 r_scbond_it 3.209 r_mcangle_it 2.109 r_mcbond_it 1.698 r_angle_refined_deg 1.563 r_rigid_bond_restr 1.561 r_angle_other_deg 0.933 r_mcbond_other 0.618 r_nbd_refined 0.212 r_symmetry_vdw_other 0.198 r_nbd_other 0.195 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.158 r_symmetry_hbond_refined 0.157 r_chiral_restr 0.111 r_symmetry_vdw_refined 0.102 r_nbtor_other 0.087 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_metal_ion_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1904 Nucleic Acid Atoms Solvent Atoms 470 Heterogen Atoms 2
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection MOSFLM data reduction CCP4 data scaling