☰ Navigation Tabs
Crystal structure of AMP-PNP complexed D-alanine-D-alanine ligase(DDL) from Yersinia pestis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 287 0.2M Sodium acetate, Bis-Tris pH7.0, PEG 8000 29%
Crystal Properties Matthews coefficient Solvent content 2.69 54.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.029 α = 90 b = 106.795 β = 90 c = 212.012 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 QUANTUM 315r 2015-03-31 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.997 PAL/PLS 5C (4A)
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 2.5 50 99.8 0.08 35.5 6.5 50546
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.5 47.69 47927 2567 99.6 0.19108 0.1883 0.24346 0.2371 RANDOM 55.212
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.961 r_dihedral_angle_4_deg 21.085 r_dihedral_angle_3_deg 17.279 r_long_range_B_refined 9.784 r_long_range_B_other 9.783 r_scangle_other 7.548 r_dihedral_angle_1_deg 6.682 r_mcangle_it 6.151 r_mcangle_other 6.151 r_scbond_it 5.049
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.961 r_dihedral_angle_4_deg 21.085 r_dihedral_angle_3_deg 17.279 r_long_range_B_refined 9.784 r_long_range_B_other 9.783 r_scangle_other 7.548 r_dihedral_angle_1_deg 6.682 r_mcangle_it 6.151 r_mcangle_other 6.151 r_scbond_it 5.049 r_scbond_other 5.049 r_mcbond_it 4.152 r_mcbond_other 4.149 r_angle_refined_deg 1.731 r_angle_other_deg 0.833 r_chiral_restr 0.089 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9041 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 133
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling PHASER phasing