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Designed Artificial Cupredoxins
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QCB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 274 2.0 M ammonium sulfate, 0.1 M sodium acetate, pH 4
Crystal Properties Matthews coefficient Solvent content 2.3 46.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.69 α = 90 b = 57.69 β = 90 c = 183.61 γ = 90
Symmetry Space Group I 41 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2016-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.00000 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.4 45.9 99.8 0.069 1 12.7 6.8 31080
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 1.4 1.42 98.8 1.446 6.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2qcb 1.4 45.9 29542 1489 99.66 0.14351 0.14162 0.18129 0.1854 RANDOM 20.519
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] -0.19 -0.19 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.582 r_sphericity_free 25.982 r_dihedral_angle_4_deg 15.845 r_sphericity_bonded 14.704 r_dihedral_angle_3_deg 13.14 r_long_range_B_refined 7.515 r_dihedral_angle_1_deg 7.412 r_scbond_it 6.608 r_rigid_bond_restr 6.026 r_long_range_B_other 5.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.582 r_sphericity_free 25.982 r_dihedral_angle_4_deg 15.845 r_sphericity_bonded 14.704 r_dihedral_angle_3_deg 13.14 r_long_range_B_refined 7.515 r_dihedral_angle_1_deg 7.412 r_scbond_it 6.608 r_rigid_bond_restr 6.026 r_long_range_B_other 5.57 r_scangle_other 5.13 r_scbond_other 4.966 r_angle_refined_deg 3.915 r_mcangle_other 3.773 r_mcangle_it 3.761 r_mcbond_it 3.034 r_mcbond_other 2.894 r_angle_other_deg 1.984 r_chiral_restr 0.193 r_bond_refined_d 0.032 r_gen_planes_refined 0.013 r_bond_other_d 0.003 r_gen_planes_other 0.003 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 924 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing