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Crystal structure of the DegP dodecamer with a modulator
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OTP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 11% PEG3350, 0.1 M tacsimate pH 3.5
Crystal Properties Matthews coefficient Solvent content 2.92 62.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 217.152 α = 90 b = 123.519 β = 118 c = 140.56 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC QUANTUM 315r 2018-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.979 PAL/PLS 5C (4A)
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 4.2 50 99.8 0.112 0.121 0.045 9.1 7.2 24531
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 4.2 4.27 100 0.665 0.718 0.269 0.921 7.1
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 (Observed) 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 3OTP 4.2 50 23246 1262 98.55 0.2516 0.2477 0.2549 0.3255 0.3281 RANDOM 51.451
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] 0.36 0.06 0.83 -0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.432 r_dihedral_angle_3_deg 19.983 r_dihedral_angle_4_deg 16.427 r_dihedral_angle_1_deg 6.036 r_angle_other_deg 1.943 r_angle_refined_deg 1.096 r_chiral_restr 0.043 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.432 r_dihedral_angle_3_deg 19.983 r_dihedral_angle_4_deg 16.427 r_dihedral_angle_1_deg 6.036 r_angle_other_deg 1.943 r_angle_refined_deg 1.096 r_chiral_restr 0.043 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17212 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing