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Crystal structure of MurD ligase in complex with UMA and ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UAG PDB ENTRY 3UAG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 PROTEIN WAS CRYSTALLIZED FROM 1.7 M (NH4)2SO4, 7% PEG 400, 100 MM HEPES, PH 7.5
Crystal Properties Matthews coefficient Solvent content 3 59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.085 α = 90 b = 65.085 β = 90 c = 134.253 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 288 CCD ADSC CCD 2006-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.52 65 96.3 0.04 31 4.6 82385 3
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 1.52 1.61 91.5 0.3 5.7 4.7
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 3UAG 1.52 65.09 80009 4287 98.6 0.189 0.188 0.1866 0.215 0.2123 RANDOM 14.98
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] 0.08 0.08 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.377 r_dihedral_angle_4_deg 16.232 r_dihedral_angle_3_deg 11.032 r_dihedral_angle_1_deg 5.82 r_scangle_it 2.968 r_scbond_it 1.887 r_angle_refined_deg 1.59 r_mcangle_it 1.258 r_mcbond_it 0.696 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.377 r_dihedral_angle_4_deg 16.232 r_dihedral_angle_3_deg 11.032 r_dihedral_angle_1_deg 5.82 r_scangle_it 2.968 r_scbond_it 1.887 r_angle_refined_deg 1.59 r_mcangle_it 1.258 r_mcbond_it 0.696 r_nbtor_refined 0.304 r_nbd_refined 0.2 r_symmetry_hbond_refined 0.17 r_symmetry_vdw_refined 0.142 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.086 r_bond_refined_d 0.043 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 3305 Nucleic Acid Atoms Solvent Atoms 484 Heterogen Atoms 81
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing