☰ Navigation Tabs
The X-ray crystal structures of D-alanyl-D-alanine ligase in complex ADP and D-cycloserine phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IOW PDB ENTRY 1IOW
Crystallization Crystal Properties Matthews coefficient Solvent content 1.9 36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.79 α = 90 b = 97.51 β = 90 c = 109.99 γ = 90
Symmetry Space Group P 21 21 21
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 CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 1.65 49 99.8 0.08 23.8 6.7 70170 2.1
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 1.65 1.71 99.7 0.66 2.1
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 1IOW 1.65 48.76 67309 2861 99.72 0.20634 0.20504 0.2344 0.23726 0.2589 RANDOM 30.664
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] -0.09 -0.49 0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.264 r_dihedral_angle_4_deg 22.193 r_dihedral_angle_3_deg 15.021 r_dihedral_angle_1_deg 5.778 r_scangle_it 3.959 r_scbond_it 2.555 r_angle_refined_deg 1.603 r_mcangle_it 1.594 r_mcbond_it 0.858 r_chiral_restr 0.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.264 r_dihedral_angle_4_deg 22.193 r_dihedral_angle_3_deg 15.021 r_dihedral_angle_1_deg 5.778 r_scangle_it 3.959 r_scbond_it 2.555 r_angle_refined_deg 1.603 r_mcangle_it 1.594 r_mcbond_it 0.858 r_chiral_restr 0.117 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_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 4661 Nucleic Acid Atoms Solvent Atoms 347 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing