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Thermococcus sibiricus cyclic 2,3-diphosphoglycerate syntethase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8ORK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.5 292.15 The best diffracting crystals grew in condition A3 of the Morpheus screen consisting of 0.12 M divalents mix, 0.1 M Buffer System 1 pH 6.5 and 30% v/v Precipitant Mix 3 (https://calibrescientific.com/en/products/MDL-MD1-47 ).
Crystal Properties Matthews coefficient Solvent content 2.81 56.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.46 α = 90 b = 80.56 β = 90 c = 82.74 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 113.15 PIXEL DECTRIS EIGER2 XE 16M 2023-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.95374 Diamond I04
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 2.28 73.83 100 1 11.6 13.7 50337
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 2.31 2.35 100 0.4 13
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.28 73.8 50336 2364 99.988 0.221 0.2186 0.2192 0.2782 0.2794 83.452
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] -2.601 -3.984 6.584
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.714 r_dihedral_angle_6_deg 14.22 r_lrange_it 10.94 r_scangle_it 8.622 r_dihedral_angle_1_deg 7.956 r_dihedral_angle_2_deg 7.516 r_mcangle_it 7.255 r_scbond_it 5.886 r_mcbond_it 4.957 r_angle_refined_deg 1.766
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.714 r_dihedral_angle_6_deg 14.22 r_lrange_it 10.94 r_scangle_it 8.622 r_dihedral_angle_1_deg 7.956 r_dihedral_angle_2_deg 7.516 r_mcangle_it 7.255 r_scbond_it 5.886 r_mcbond_it 4.957 r_angle_refined_deg 1.766 r_nbtor_refined 0.296 r_nbd_refined 0.217 r_symmetry_nbd_refined 0.166 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.12 r_symmetry_xyhbond_nbd_refined 0.117 r_bond_refined_d 0.006 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6766 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing