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Crystal Structure of L-N-carbamoylase from Geobacillus stearothermophilus CECT43
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z2L PDB entry 1Z2L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 15 % iso-propanol, 0.1 M sodium cacodylate pH 6.5 and 0.6 M trisodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.67 53.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.208 α = 90 b = 211.683 β = 90 c = 43.091 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD BRUKER SMART 6000 Kappa configuration 2006-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.75 73.89 99.1 0.1238 0.1238 15.05 7.26 25512 25512
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.85 91.5 0.2578 0.2578 4.16 3.92
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 PDB entry 1Z2L 2.75 20 23771 1271 98.52 0.1968 0.19266 0.194 0.27579 0.2746 RANDOM 14.701
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] 1.82 -0.26 -1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.85 r_dihedral_angle_4_deg 21.874 r_dihedral_angle_3_deg 19.071 r_dihedral_angle_1_deg 6.284 r_scangle_it 2.695 r_scbond_it 1.581 r_angle_refined_deg 1.556 r_mcangle_it 1.075 r_mcbond_it 0.604 r_chiral_restr 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.85 r_dihedral_angle_4_deg 21.874 r_dihedral_angle_3_deg 19.071 r_dihedral_angle_1_deg 6.284 r_scangle_it 2.695 r_scbond_it 1.581 r_angle_refined_deg 1.556 r_mcangle_it 1.075 r_mcbond_it 0.604 r_chiral_restr 0.098 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5993 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction PROTEUM PLUS data collection SAINT data reduction PROTEUM PLUS data scaling MOLREP phasing