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Crystal structure of L-N-Carbamoylase from Sinorhizobium meliloti mutant L217G/F329C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 20 mM K,Na-phosphate, 0.1 M Bis-Tris Propane, 20 % PEG3350
Crystal Properties Matthews coefficient Solvent content 2 39.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.569 α = 90 b = 42.047 β = 94.78 c = 137.211 γ = 90
Symmetry Space Group I 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 PIXEL DECTRIS PILATUS3 2M 2022-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.9655 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.3 99.23 98.7 0.117 0.128 0.052 0.996 9.9 5.9 33664
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 2.3 2.38 89.8 0.914 1.048 0.497 0.679 4.1
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 AF model 2.3 99.23 31851 1807 98.51 0.1761 0.1728 0.1802 0.2382 0.2413 RANDOM 50.557
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] 0.75 -2.77 2.66 -2.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.788 r_dihedral_angle_3_deg 16.118 r_dihedral_angle_1_deg 7.358 r_angle_refined_deg 1.497 r_angle_other_deg 0.492 r_chiral_restr 0.063 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6188 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 41
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction