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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 2.92 57.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.72 α = 90 b = 57.72 β = 90 c = 183.46 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 1.0000 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 1.7 45.9 66.9 0.092 1 9.7 5.1 11863
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 1.7 1.73 64.3 1.997 0.7 4.3
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 1.7 45.9 11233 589 67.14 0.17488 0.17182 0.23397 0.2251 RANDOM 23.625
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] -0.25 -0.25 0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.324 r_dihedral_angle_4_deg 19.268 r_dihedral_angle_3_deg 13.143 r_sphericity_free 12.044 r_sphericity_bonded 10.914 r_dihedral_angle_1_deg 7.62 r_scangle_other 6.288 r_long_range_B_other 6.087 r_long_range_B_refined 6.064 r_scbond_it 4.944
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.324 r_dihedral_angle_4_deg 19.268 r_dihedral_angle_3_deg 13.143 r_sphericity_free 12.044 r_sphericity_bonded 10.914 r_dihedral_angle_1_deg 7.62 r_scangle_other 6.288 r_long_range_B_other 6.087 r_long_range_B_refined 6.064 r_scbond_it 4.944 r_scbond_other 4.916 r_mcangle_other 4.336 r_rigid_bond_restr 4.328 r_mcangle_it 4.308 r_mcbond_it 3.767 r_mcbond_other 3.593 r_angle_refined_deg 2.523 r_angle_other_deg 1.062 r_chiral_restr 0.125 r_bond_refined_d 0.025 r_gen_planes_refined 0.01 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 924 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing