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Crystal structure of putrescine transcarbamylase from Enterococcus faecalis lacking its C-terminal Helix, with bound N5-(phosphonoacetyl) -L-ornithine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4A8H PDB ENTRY 4A8H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.2 M MAGNESIUM CHLORIDE, 30% POLYETHYLENE GLYCOL 400, 0.1 M HEPES, PH 7.5, 1 MM N5-(PHOSPHONOACETYL)-L-ORNITHINE
Crystal Properties Matthews coefficient Solvent content 3.03 59.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.99 α = 90 b = 89.99 β = 90 c = 184.32 γ = 120
Symmetry Space Group P 63 2 2
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 ADSC QUANTUM 315r 2010-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.59 40 100 0.08 5.7 10.1 60518 2 14.7
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 1.59 30 99.8 0.37 2.1 10.1
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 PDB ENTRY 4A8H 1.59 30 57317 3050 99.85 0.16308 0.16218 0.1811 0.18015 0.2002 RANDOM 13.539
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] -0.28 -0.14 -0.28 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.587 r_dihedral_angle_4_deg 17.874 r_dihedral_angle_3_deg 11.667 r_dihedral_angle_1_deg 5.273 r_scangle_it 2.3 r_scbond_it 1.441 r_angle_refined_deg 1.133 r_angle_other_deg 0.926 r_mcangle_it 0.736 r_mcbond_it 0.399
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.587 r_dihedral_angle_4_deg 17.874 r_dihedral_angle_3_deg 11.667 r_dihedral_angle_1_deg 5.273 r_scangle_it 2.3 r_scbond_it 1.441 r_angle_refined_deg 1.133 r_angle_other_deg 0.926 r_mcangle_it 0.736 r_mcbond_it 0.399 r_mcbond_other 0.102 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2446 Nucleic Acid Atoms Solvent Atoms 387 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing