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Crystal structure of activity improved formolase variant K1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6M2Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M sodium citrate 5.5, 20 % w/v PEG 3000
Crystal Properties Matthews coefficient Solvent content 2.38 48.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.271 α = 90 b = 99.376 β = 90 c = 110.092 γ = 90
Symmetry Space Group I 2 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 PIXEL DECTRIS PILATUS 6M 2022-01-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.987 SSRF BL10U2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.05 25 99.5 0.987 13.4 6.3 34208
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.12 100 0.889 3.12
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.05 24.6 32454 1719 98.53 0.18105 0.17781 0.1881 0.24141 0.2402 RANDOM 27.749
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] -3.04 2.39 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.109 r_dihedral_angle_4_deg 21.169 r_dihedral_angle_3_deg 15.347 r_dihedral_angle_1_deg 9.224 r_long_range_B_refined 5.604 r_long_range_B_other 5.529 r_scangle_other 3.824 r_mcangle_it 2.611 r_mcangle_other 2.611 r_scbond_it 2.607
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.109 r_dihedral_angle_4_deg 21.169 r_dihedral_angle_3_deg 15.347 r_dihedral_angle_1_deg 9.224 r_long_range_B_refined 5.604 r_long_range_B_other 5.529 r_scangle_other 3.824 r_mcangle_it 2.611 r_mcangle_other 2.611 r_scbond_it 2.607 r_scbond_other 2.559 r_mcbond_it 1.907 r_mcbond_other 1.906 r_angle_refined_deg 1.576 r_angle_other_deg 1.377 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3934 Nucleic Acid Atoms Solvent Atoms 365 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing