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All Phe-Azurin variant - F15W
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AZU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20 mg/mL protein in 0.1 M NaOAc (pH 5.0), 26.5-29% PEG 4000, 100 mM lithium nitrate, 10 mM copper sulfate, and 100 mM tris (pH 8.0)
Crystal Properties Matthews coefficient Solvent content 2.17 43.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.782 α = 90 b = 59.525 β = 90 c = 74.342 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 PIXEL DECTRIS EIGER X 16M 2021-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.03324 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 1.85 44.14 96.7 0.038 0.054 0.997 11.4 1.9 20615
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.89 76.6 0.213 0.89 3.1 1.8
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-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4AZU 1.85 44.14 20615 1038 96.377 0.192 0.1891 0.2433 0.2606 RANDOM 26.607
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] -0.011 -0.075 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.788 r_dihedral_angle_other_3_deg 18.518 r_dihedral_angle_3_deg 14.163 r_dihedral_angle_4_deg 9.434 r_dihedral_angle_1_deg 7.634 r_lrange_it 5.865 r_lrange_other 5.858 r_scangle_it 4.51 r_scangle_other 4.505 r_mcangle_other 3.393
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.788 r_dihedral_angle_other_3_deg 18.518 r_dihedral_angle_3_deg 14.163 r_dihedral_angle_4_deg 9.434 r_dihedral_angle_1_deg 7.634 r_lrange_it 5.865 r_lrange_other 5.858 r_scangle_it 4.51 r_scangle_other 4.505 r_mcangle_other 3.393 r_mcangle_it 3.39 r_scbond_it 2.891 r_scbond_other 2.891 r_mcbond_it 2.256 r_mcbond_other 2.241 r_angle_refined_deg 1.529 r_angle_other_deg 1.393 r_metal_ion_refined 0.547 r_nbd_refined 0.229 r_nbd_other 0.215 r_symmetry_nbd_refined 0.206 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.164 r_symmetry_xyhbond_nbd_refined 0.139 r_xyhbond_nbd_refined 0.127 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.066 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1948 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement Aimless data scaling MOLREP phasing Coot model building