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Azurin fom Pseudomonas aeruginosa treated with hydrosulfide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AZU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 30% PEG 4000, 100 mM NaHEPES pH 6,5, 200 mM CaCl2, 10 mM Na2S. Cryoprotectant: 10% PEG 4000, 20% PEG 400, 100 mM NaHEPES pH 6,5, 200 mM CaCl2
Crystal Properties Matthews coefficient Solvent content 2.18 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.736 α = 90 b = 59.781 β = 90.38 c = 79.727 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS 6M-F mirror 2017-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 0.81410 PETRA III, DESY P11
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 1.59 50 98.8 0.033 0.046 0.998 10.8 6.7 62899 30
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.59 1.69 96 1.015 1.099 0.646 1.46 6.7
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 1AZU 1.6 47.83 60454 2089 99.17 0.1933 0.19161 0.1983 0.24273 0.2487 RANDOM 29.679
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] -2.79 -0.36 1.23 1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.706 r_dihedral_angle_3_deg 15.541 r_dihedral_angle_4_deg 12.03 r_dihedral_angle_1_deg 7.176 r_long_range_B_refined 5.996 r_long_range_B_other 5.929 r_angle_refined_deg 2.729 r_scangle_other 2.617 r_mcangle_it 1.832 r_mcangle_other 1.832
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.706 r_dihedral_angle_3_deg 15.541 r_dihedral_angle_4_deg 12.03 r_dihedral_angle_1_deg 7.176 r_long_range_B_refined 5.996 r_long_range_B_other 5.929 r_angle_refined_deg 2.729 r_scangle_other 2.617 r_mcangle_it 1.832 r_mcangle_other 1.832 r_scbond_it 1.747 r_scbond_other 1.747 r_angle_other_deg 1.306 r_mcbond_it 1.179 r_mcbond_other 1.177 r_chiral_restr 0.18 r_bond_refined_d 0.031 r_gen_planes_refined 0.015 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3853 Nucleic Acid Atoms Solvent Atoms 427 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing