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Structure of a cavity mutant (H117G) of Pseudomonas aeruginosa azurin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E67 PDB ENTRY 1E67
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 100 MM TRIS-HCL PH 8.5 AND 20% (W/V) POLYETHYLENE GLYCOL (PEG) 8000
Crystal Properties Matthews coefficient Solvent content 2.3 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.664 α = 109.25 b = 49.718 β = 94.96 c = 66.065 γ = 99.24
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate MIRRORS 2004-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR78
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 2.85 60 88.2 0.09 9.4 2.7 10566 1.8 62.5
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 2.85 2.95 36 0.34 1.8 1.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1E67 2.83 61.66 2 10566 494 88.2 0.194 0.192 0.1914 0.233 0.226 RANDOM 30.6
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] -0.791 -3.624 -0.822 -1.062 0.363 0.786
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.469 r_dihedral_angle_3_deg 17.91 r_dihedral_angle_1_deg 6.866 r_dihedral_angle_4_deg 5.491 r_mcangle_it 2.445 r_scangle_it 2.117 r_mcbond_it 1.543 r_scbond_it 1.464 r_angle_refined_deg 1.07 r_symmetry_vdw_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.469 r_dihedral_angle_3_deg 17.91 r_dihedral_angle_1_deg 6.866 r_dihedral_angle_4_deg 5.491 r_mcangle_it 2.445 r_scangle_it 2.117 r_mcbond_it 1.543 r_scbond_it 1.464 r_angle_refined_deg 1.07 r_symmetry_vdw_refined 0.316 r_nbtor_refined 0.313 r_nbd_refined 0.201 r_xyhbond_nbd_refined 0.154 r_symmetry_hbond_refined 0.136 r_chiral_restr 0.077 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3872 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing