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Orf1-E312A-glycine-glycylthricin
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 3.36 63.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.294 α = 89.798 b = 108.08 β = 89.976 c = 133.463 γ = 96.345
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 2022-08-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 07A 1 NSRRC TPS 07A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.365 30 99.3 0.086 0.993 17.9 5.1 231222
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.37 2.45 99 0.631 0.826 2.4
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 7XQA 2.365 29.672 222660 10823 94.942 0.209 0.2074 0.2104 0.2334 0.2342 41.967
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] -0.038 0.121 -0.033 -0.013 -0.2 0.023
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.496 r_dihedral_angle_3_deg 16.511 r_dihedral_angle_4_deg 13.75 r_dihedral_angle_1_deg 6.715 r_lrange_it 6.629 r_lrange_other 6.626 r_scangle_it 4.813 r_scangle_other 4.813 r_mcangle_it 4.119 r_mcangle_other 4.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.496 r_dihedral_angle_3_deg 16.511 r_dihedral_angle_4_deg 13.75 r_dihedral_angle_1_deg 6.715 r_lrange_it 6.629 r_lrange_other 6.626 r_scangle_it 4.813 r_scangle_other 4.813 r_mcangle_it 4.119 r_mcangle_other 4.118 r_scbond_it 2.968 r_scbond_other 2.968 r_mcbond_it 2.635 r_mcbond_other 2.635 r_angle_refined_deg 1.372 r_angle_other_deg 1.227 r_chiral_restr 0.324 r_nbd_other 0.278 r_symmetry_nbd_refined 0.244 r_nbd_refined 0.182 r_symmetry_nbd_other 0.176 r_nbtor_refined 0.152 r_xyhbond_nbd_refined 0.13 r_symmetry_nbtor_other 0.082 r_symmetry_xyhbond_nbd_refined 0.06 r_ncsr_local_group_19 0.03 r_ncsr_local_group_40 0.03 r_ncsr_local_group_4 0.029 r_ncsr_local_group_6 0.029 r_ncsr_local_group_18 0.029 r_ncsr_local_group_1 0.027 r_ncsr_local_group_5 0.027 r_ncsr_local_group_41 0.027 r_ncsr_local_group_8 0.026 r_ncsr_local_group_38 0.026 r_ncsr_local_group_20 0.025 r_ncsr_local_group_17 0.024 r_ncsr_local_group_28 0.024 r_ncsr_local_group_33 0.024 r_ncsr_local_group_15 0.021 r_ncsr_local_group_7 0.02 r_ncsr_local_group_12 0.02 r_ncsr_local_group_43 0.02 r_ncsr_local_group_16 0.019 r_ncsr_local_group_46 0.019 r_ncsr_local_group_2 0.018 r_ncsr_local_group_32 0.018 r_ncsr_local_group_14 0.017 r_ncsr_local_group_24 0.017 r_ncsr_local_group_13 0.016 r_ncsr_local_group_26 0.016 r_ncsr_local_group_37 0.016 r_ncsr_local_group_45 0.016 r_ncsr_local_group_10 0.015 r_ncsr_local_group_25 0.015 r_ncsr_local_group_44 0.015 r_ncsr_local_group_22 0.014 r_ncsr_local_group_29 0.014 r_ncsr_local_group_35 0.014 r_ncsr_local_group_42 0.014 r_ncsr_local_group_27 0.013 r_ncsr_local_group_9 0.011 r_ncsr_local_group_34 0.011 r_ncsr_local_group_3 0.01 r_ncsr_local_group_21 0.01 r_ncsr_local_group_30 0.01 r_ncsr_local_group_36 0.01 r_ncsr_local_group_31 0.008 r_ncsr_local_group_23 0.007 r_ncsr_local_group_39 0.007 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_ncsr_local_group_11 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 29016 Nucleic Acid Atoms Solvent Atoms 686 Heterogen Atoms 704
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing