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Crystal structure of Glutamine Synthetase-apo
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7TF7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 0.1M NaCl, 0.1M BICINE pH 9.0, 5mM MgCl2, 20% v/v polyethylene glycol monomethyl ether 550
Crystal Properties Matthews coefficient Solvent content 4.06 71.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 260.909 α = 90 b = 260.909 β = 90 c = 154.18 γ = 90
Symmetry Space Group P 43 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 100 PIXEL DECTRIS PILATUS 6M 2024-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0 ELETTRA 11.2C
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 3.4 99.59 98.5 0.967 9 6.8 72108
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 3.4 3.47 98.1 0.36 2.6 7.1
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3.4 93.215 72012 3543 98.14 0.235 0.2327 0.2346 0.2702 0.2702 RANDOM 111.481
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] -0.338 -0.338 0.676
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 23.761 r_dihedral_angle_2_deg 19.384 r_dihedral_angle_6_deg 15.551 r_lrange_it 15.023 r_lrange_other 15.022 r_mcangle_it 7.949 r_scangle_it 7.949 r_scangle_other 7.949 r_mcangle_other 7.948 r_dihedral_angle_1_deg 6.846
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 23.761 r_dihedral_angle_2_deg 19.384 r_dihedral_angle_6_deg 15.551 r_lrange_it 15.023 r_lrange_other 15.022 r_mcangle_it 7.949 r_scangle_it 7.949 r_scangle_other 7.949 r_mcangle_other 7.948 r_dihedral_angle_1_deg 6.846 r_mcbond_it 4.721 r_mcbond_other 4.721 r_scbond_it 4.652 r_scbond_other 4.652 r_angle_refined_deg 2.16 r_angle_other_deg 0.73 r_symmetry_xyhbond_nbd_refined 0.284 r_nbd_other 0.274 r_symmetry_nbd_refined 0.26 r_nbd_refined 0.246 r_metal_ion_refined 0.232 r_symmetry_nbd_other 0.228 r_nbtor_refined 0.2 r_ncsr_local_group_9 0.184 r_ncsr_local_group_5 0.179 r_ncsr_local_group_8 0.178 r_ncsr_local_group_14 0.178 r_ncsr_local_group_10 0.175 r_ncsr_local_group_2 0.174 r_ncsr_local_group_7 0.174 r_ncsr_local_group_6 0.172 r_ncsr_local_group_11 0.171 r_ncsr_local_group_13 0.17 r_ncsr_local_group_12 0.169 r_ncsr_local_group_4 0.168 r_ncsr_local_group_15 0.166 r_ncsr_local_group_1 0.159 r_ncsr_local_group_3 0.157 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.102 r_symmetry_nbtor_other 0.091 r_xyhbond_nbd_other 0.051 r_symmetry_xyhbond_nbd_other 0.043 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21818 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement autoPX data processing iMOSFLM data reduction Aimless data scaling MOLREP phasing