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Computational Design of an Unnatural Amino Acid Metalloprotein with Atomic Level Accuracy
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IGS PDB ENTRY 1IGS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 6.5 298 1.8 M ammonium sulfate, 5% PEG3350, pH 6.5, EVAPORATION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.18 43.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.265 α = 90 b = 60.265 β = 90 c = 123.566 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 98 IMAGE PLATE RIGAKU RAXIS IV++ Varimax HR 2012-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.3 123.6 93.1 0.041 24.3 3.2 22369 20826 2 20.86
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 96.9 0.079 3.3 2195
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1IGS 2.3 123.57 19758 19758 1068 93.11 0.21164 0.21164 0.2087 0.2072 0.2636 0.2596 RANDOM 19.841
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] 0.34 0.17 0.34 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.074 r_dihedral_angle_4_deg 19.346 r_dihedral_angle_3_deg 17.353 r_dihedral_angle_1_deg 6.281 r_scangle_it 3.385 r_scbond_it 2.03 r_angle_refined_deg 1.455 r_mcangle_it 1.226 r_mcbond_it 0.645 r_chiral_restr 0.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.074 r_dihedral_angle_4_deg 19.346 r_dihedral_angle_3_deg 17.353 r_dihedral_angle_1_deg 6.281 r_scangle_it 3.385 r_scbond_it 2.03 r_angle_refined_deg 1.455 r_mcangle_it 1.226 r_mcbond_it 0.645 r_chiral_restr 0.101 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3988 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 47
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling