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Carboxypeptidase G2 modified with a versatile bioconjugate for metalloprotein design
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CG2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 Reservoir consisted of 750 uL of 0.2 M Tris pH 7.5, 10% PEG 3350, and 5% glycerol. 2 uL of reservoir solution was mixed with 2 uL of protein solution, consisting of 4.7 mg/mL CPG2 in 50 mM Tris 100 mM NaCl pH 7.4 supplemented with 0.1 M ZnSO4
Crystal Properties Matthews coefficient Solvent content 2.4 48.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.12 α = 90 b = 188.46 β = 90.17 c = 124.5 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 93 PIXEL DECTRIS PILATUS3 6M Adjustable focus K-B pair Si plus Pt, Rh coatings 2019-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim 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 3.11 41.5 99.87 0.389 0.389 0.423 0.164 0.977 4.3 6.6 59536
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.11 3.16 99.93 1.949 1.949 2.106 0.793 0.358 1.1 6.91
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1CG2 3.11 41.5 59515 2981 99.784 0.273 0.2713 0.2707 0.3086 0.3053 62.855
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] -4.783 1.683 1.256 3.517
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.754 r_dihedral_angle_4_deg 13.485 r_dihedral_angle_3_deg 12.918 r_dihedral_angle_other_3_deg 4.714 r_dihedral_angle_1_deg 4.069 r_lrange_it 3.973 r_lrange_other 3.955 r_mcangle_it 1.357 r_mcangle_other 1.357 r_angle_other_deg 1.145
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.754 r_dihedral_angle_4_deg 13.485 r_dihedral_angle_3_deg 12.918 r_dihedral_angle_other_3_deg 4.714 r_dihedral_angle_1_deg 4.069 r_lrange_it 3.973 r_lrange_other 3.955 r_mcangle_it 1.357 r_mcangle_other 1.357 r_angle_other_deg 1.145 r_angle_refined_deg 1.144 r_scangle_it 1.002 r_scangle_other 1.002 r_mcbond_it 0.762 r_mcbond_other 0.762 r_scbond_it 0.654 r_scbond_other 0.653 r_nbd_other 0.297 r_symmetry_nbd_refined 0.278 r_symmetry_nbd_other 0.222 r_nbd_refined 0.219 r_symmetry_xyhbond_nbd_refined 0.176 r_xyhbond_nbd_refined 0.17 r_nbtor_refined 0.152 r_metal_ion_refined 0.135 r_ncsr_local_group_10 0.099 r_ncsr_local_group_1 0.096 r_symmetry_metal_ion_refined 0.095 r_ncsr_local_group_2 0.094 r_ncsr_local_group_8 0.094 r_ncsr_local_group_4 0.092 r_ncsr_local_group_9 0.092 r_ncsr_local_group_15 0.091 r_symmetry_xyhbond_nbd_other 0.09 r_ncsr_local_group_14 0.09 r_ncsr_local_group_3 0.085 r_ncsr_local_group_13 0.085 r_ncsr_local_group_18 0.085 r_ncsr_local_group_25 0.085 r_ncsr_local_group_11 0.082 r_ncsr_local_group_19 0.082 r_ncsr_local_group_24 0.081 r_symmetry_nbtor_other 0.08 r_ncsr_local_group_5 0.08 r_ncsr_local_group_12 0.08 r_ncsr_local_group_16 0.08 r_ncsr_local_group_17 0.079 r_ncsr_local_group_22 0.079 r_ncsr_local_group_6 0.078 r_ncsr_local_group_20 0.076 r_ncsr_local_group_23 0.076 r_ncsr_local_group_27 0.072 r_ncsr_local_group_26 0.071 r_ncsr_local_group_21 0.07 r_ncsr_local_group_7 0.069 r_ncsr_local_group_28 0.064 r_chiral_restr 0.022 r_bond_refined_d 0.003 r_gen_planes_refined 0.002 r_bond_other_d r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21355 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement xia2 data reduction PHASER phasing xia2 data scaling