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Crystal structure of Weissella viridescens FemXVv non-ribosomal amino acid transferase in complex with a peptidyl-RNA conjugate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GKR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 295 0.1M Tris-sodium citrate buffer, 0.2M ammonium acetate, 33% polyethylene glycol 4k, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.38 48.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.13 α = 90 b = 101.77 β = 102.6 c = 46.32 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS 6M mirrors 2012-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9791 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.66 38.12 99.5 0.04 23.8 3.7 44718 44718 -3 23.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.66 1.76 98.1 0.189 6.9 3.5 7126
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3GKR 1.66 38.12 44718 42482 2236 99.54 0.178 0.17661 0.17487 0.1665 0.20935 0.201 RANDOM 17.328
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] -0.95 0.41 -1.07 1.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.099 r_dihedral_angle_4_deg 21.742 r_dihedral_angle_3_deg 12.135 r_dihedral_angle_1_deg 5.842 r_angle_refined_deg 2.342 r_chiral_restr 0.17 r_bond_refined_d 0.024 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2727 Nucleic Acid Atoms 68 Solvent Atoms 296 Heterogen Atoms 49
Software Software Software Name Purpose MX data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling