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Crystal structure of wild-type L-N-Carbamoylase from Sinorhizobium meliloti
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 6.5 294 0.2 M sodium acetate, 0.1 M Bis-tris propane and 20 % PEG3350
Crystal Properties Matthews coefficient Solvent content 2 38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.25 α = 90 b = 41.801 β = 94.08 c = 133.996 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 PILATUS 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 1.75 45.53 99.5 0.088 0.095 0.037 0.997 13.3 6.5 74615
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 1.75 1.78 97.4 0.778 0.848 0.332 0.836 6.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT AF model 1.75 43.22 70922 3687 99.46 0.1513 0.1495 0.1855 0.1817 RANDOM 25.558
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] -1.81 -1.21 1.49 0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.967 r_dihedral_angle_2_deg 8.149 r_dihedral_angle_1_deg 6.873 r_angle_refined_deg 1.412 r_angle_other_deg 0.516 r_chiral_restr 0.211 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6221 Nucleic Acid Atoms Solvent Atoms 460 Heterogen Atoms 56
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction