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A small alarmone hydrolase TdActApo2 mutant - T78N
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GNI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.22 mM TdRel-D78N protein in the buffer of 1 mM MnCl2, 25 mM Tris-HCl pH 8.0, and 200 mM NaCl was mixed 1:1 ratio with the precipitant containing 0.2 M NH4Cl and 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.63 53.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.286 α = 90 b = 69.189 β = 93.015 c = 132.07 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 100 PIXEL DECTRIS EIGER2 X 16M 2021-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976238 Diamond I03
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 2.38 61.345 100 0.999 10.4 11.7 44562
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 2.39 2.47 100 0.604 1 11.4
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 FREE R-VALUE 3gni 2.38 61.278 44544 2212 99.978 0.193 0.1907 0.1925 0.2269 0.2287 63.939
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] 4.215 -0.998 -0.017 -4.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.488 r_dihedral_angle_4_deg 21.442 r_dihedral_angle_3_deg 17.968 r_lrange_it 12.855 r_lrange_other 12.841 r_scangle_it 10.131 r_scangle_other 10.13 r_mcangle_it 9.43 r_mcangle_other 9.43 r_scbond_it 6.996
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.488 r_dihedral_angle_4_deg 21.442 r_dihedral_angle_3_deg 17.968 r_lrange_it 12.855 r_lrange_other 12.841 r_scangle_it 10.131 r_scangle_other 10.13 r_mcangle_it 9.43 r_mcangle_other 9.43 r_scbond_it 6.996 r_scbond_other 6.995 r_mcbond_other 6.629 r_mcbond_it 6.628 r_dihedral_angle_1_deg 6.242 r_angle_refined_deg 1.64 r_angle_other_deg 1.37 r_symmetry_nbd_refined 0.402 r_symmetry_xyhbond_nbd_refined 0.382 r_nbd_refined 0.231 r_nbd_other 0.188 r_symmetry_nbd_other 0.17 r_xyhbond_nbd_refined 0.17 r_nbtor_refined 0.167 r_ncsr_local_group_6 0.086 r_ncsr_local_group_3 0.084 r_ncsr_local_group_5 0.083 r_chiral_restr 0.082 r_symmetry_nbtor_other 0.082 r_ncsr_local_group_2 0.082 r_ncsr_local_group_1 0.08 r_ncsr_local_group_4 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5493 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing