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Crystal Structure of Penicillin-binding protein 1A (Pbp1a) from Chlamydia trachomatis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JCH MR-rosetta based on PDB entries 2jch-A, 5u2g-B, 3vma-A, 4oon-A, 2olv_B experimental model PDB 5U2G MR-rosetta based on PDB entries 2jch-A, 5u2g-B, 3vma-A, 4oon-A, 2olv_B experimental model PDB 3VMA MR-rosetta based on PDB entries 2jch-A, 5u2g-B, 3vma-A, 4oon-A, 2olv_B experimental model PDB 4OON MR-rosetta based on PDB entries 2jch-A, 5u2g-B, 3vma-A, 4oon-A, 2olv_B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 287 RigakuReagents Wizard3/4 screen condition B8: 100mM HEPES/NaOH pH 7.0, 10% (w/V) PEG 8000: ChtrB.19241.a.D11.PD228392 at 15.5mg/ml + 1mM imipenem: tray: 313782 b8: cryo: 25% EG: puck HIO1-1.
Crystal Properties Matthews coefficient Solvent content 2.42 49.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 175.79 α = 90 b = 175.79 β = 90 c = 339.7 γ = 120
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 RAYONIX MX-300 Beryllium Lenses 2020-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 3.1 50 99.8 0.112 0.128 0.995 11.77 4.35 36840 49.068
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.18 100 0.58 0.658 0.82 2.95 4.437
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE MR-rosetta based on PDB entries 2jch-A, 5u2g-B, 3vma-A, 4oon-A, 2olv_B 3.1 47.6 1.35 36832 2016 99.8 0.1936 0.1923 0.1923 0.2159 0.2156 61.92
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.9451 f_angle_d 0.557 f_chiral_restr 0.0452 f_plane_restr 0.0041 f_bond_d 0.0027
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8883 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 50
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction MR-Rosetta phasing Coot model building