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F316A-glycine-streptothricin F complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7XQA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.1 M Tris-HCl pH8.5, 0.2 M KBr, 8 % PEG 550 MME and 8 % PEG 20000
Crystal Properties Matthews coefficient Solvent content 3.37 63.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.31 α = 90.009 b = 106.404 β = 90.013 c = 135.541 γ = 96.214
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD RAYONIX MX300-HS 2022-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 1 NSRRC TPS 05A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 30 98.2 0.081 0.093 0.045 17.5 4.3 352119
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.12 96.8 0.617 0.712 0.352 2.4 3.9
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 7XQA 2.052 29.919 347963 17603 96.908 0.189 0.1876 0.1941 0.2082 0.2127 29.873
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] -0.039 -0.016 0.046 0.205 0.128 -0.167
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.282 r_dihedral_angle_3_deg 15.633 r_dihedral_angle_4_deg 13.492 r_dihedral_angle_1_deg 6.63 r_lrange_it 6.132 r_lrange_other 6.092 r_scangle_it 4.551 r_scangle_other 4.551 r_mcangle_it 3.117 r_mcangle_other 3.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.282 r_dihedral_angle_3_deg 15.633 r_dihedral_angle_4_deg 13.492 r_dihedral_angle_1_deg 6.63 r_lrange_it 6.132 r_lrange_other 6.092 r_scangle_it 4.551 r_scangle_other 4.551 r_mcangle_it 3.117 r_mcangle_other 3.117 r_scbond_it 2.882 r_scbond_other 2.882 r_mcbond_it 2.09 r_mcbond_other 2.09 r_angle_refined_deg 1.488 r_angle_other_deg 1.344 r_chiral_restr_other 1.157 r_nbd_other 0.296 r_symmetry_nbd_refined 0.202 r_nbd_refined 0.191 r_symmetry_nbd_other 0.178 r_nbtor_refined 0.155 r_xyhbond_nbd_refined 0.141 r_symmetry_xyhbond_nbd_refined 0.133 r_chiral_restr 0.079 r_symmetry_nbtor_other 0.078 r_ncsr_local_group_2 0.06 r_ncsr_local_group_15 0.06 r_ncsr_local_group_6 0.059 r_ncsr_local_group_24 0.059 r_ncsr_local_group_1 0.052 r_ncsr_local_group_10 0.052 r_ncsr_local_group_14 0.051 r_ncsr_local_group_16 0.051 r_ncsr_local_group_26 0.051 r_ncsr_local_group_5 0.05 r_ncsr_local_group_7 0.05 r_ncsr_local_group_8 0.05 r_ncsr_local_group_12 0.05 r_ncsr_local_group_21 0.05 r_ncsr_local_group_23 0.05 r_ncsr_local_group_25 0.05 r_ncsr_local_group_18 0.049 r_ncsr_local_group_28 0.049 r_ncsr_local_group_3 0.048 r_ncsr_local_group_9 0.048 r_ncsr_local_group_19 0.048 r_ncsr_local_group_27 0.048 r_ncsr_local_group_20 0.047 r_ncsr_local_group_13 0.046 r_ncsr_local_group_11 0.013 r_ncsr_local_group_22 0.013 r_ncsr_local_group_17 0.011 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_ncsr_local_group_4 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 29136 Nucleic Acid Atoms Solvent Atoms 1827 Heterogen Atoms 744
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing