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MYCOBACTERIUM DIAMINOPIMELATE DICARBOXYLASE (LysA)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 4 UL HANGING DROPS (2 UL OF DAPDC 10 MG/ML CONTAINING 5MM OF LYSINE COMBINED WITH 2 UL OF WELL SOLUTION) WERE EQUILIBRATED AGAINST 500 UL OF WELL SOLUTION (24% PEG-MME 5K, 0.1M MES BUFFER PH6.3 AND 60 MM AMMONIUM SULFATE), pH 6.50
Crystal Properties Matthews coefficient Solvent content 4.1 70
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.56 α = 90 b = 111.56 β = 90 c = 237.673 γ = 90
Symmetry Space Group P 41 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 120 CCD ADSC CCD MIRROR 2002-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-ID-B APS 14-ID-B
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 2.8 65.7 99.9 0.028 28.2 22.6 813664
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 2.8 2.87 99.8 0.136 7.5 22
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-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.8 25 35855 1886 100 0.195 0.193 0.2031 0.248 RANDOM 38.37
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] 0.26 0.26 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.849 r_scangle_it 4.744 r_scbond_it 2.847 r_mcangle_it 1.788 r_angle_refined_deg 1.699 r_mcbond_it 0.98 r_angle_other_deg 0.974 r_nbd_other 0.267 r_symmetry_vdw_other 0.264 r_nbd_refined 0.237
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.849 r_scangle_it 4.744 r_scbond_it 2.847 r_mcangle_it 1.788 r_angle_refined_deg 1.699 r_mcbond_it 0.98 r_angle_other_deg 0.974 r_nbd_other 0.267 r_symmetry_vdw_other 0.264 r_nbd_refined 0.237 r_symmetry_hbond_refined 0.228 r_xyhbond_nbd_refined 0.173 r_chiral_restr 0.162 r_symmetry_vdw_refined 0.112 r_nbtor_other 0.106 r_bond_refined_d 0.03 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 6641 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 10
Software Software Software Name Purpose TEXTAL model building SCALEPACK data scaling SOLVE phasing SHARP phasing DM phasing TEXTAL phasing REFMAC refinement