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Engineered sperm whale myoglobin-based carbene transferase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JW8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 296 A crystal was grown by mixing 1 ul of reservoir buffer (2 M ammonium sulfate, 0.2 M Tris pH 8.6) with 1 ul of protein in buffer (20 mM Tris pH 8.0, 1 mM EDTA). The crystal was cryoprotected by soaking it in a drop containing reservoir buffer supplemented with 25% sucrose for 5 minutes prior to being flash-cooled in liquid nitrogen
Crystal Properties Matthews coefficient Solvent content 3.13 60.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.78 α = 90 b = 90.78 β = 90 c = 45.58 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 100 PIXEL DECTRIS PILATUS 6M 2017-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.9768 CHESS F1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.1 39.43 87.7 0.051 0.025 0.999 13.5 4.3 76057
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.1 1.16 40.4 0.448 0.407 0.617 1.4
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1JW8 1.1 32.163 1.34 76038 3765 87.53 0.1273 0.1263 0.1301 0.1458 0.1495
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 29.707 f_angle_d 1.134 f_chiral_restr 0.076 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1216 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 81
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction SCALA data scaling PHENIX phasing