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mycobacterium diaminopimelate dicarboxylase (lysa)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HKW PDB ENTRY 1HKW
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). THESE CRYSTALS WERE SOAKED FOR 3 HRS IN IN MOTHER LIQUOR CONTAINING 0.2 MM PLP. THE CRYSTALS ARE DISTINCTLY YELLOW., pH 6.50
Crystal Properties Matthews coefficient Solvent content 3.9 67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.452 α = 90 b = 111.452 β = 90 c = 238.253 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 DOUBLE MONO 2002-11-15 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 2.6 65.5 99.8 0.081 14.6 6.2 44373
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 2.6 2.67 94 0.405 3.1 6.2
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1HKW 2.6 18 44373 2374 99.8 0.227 0.224 0.268 RANDOM 47.48
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 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.95 r_scangle_it 4.474 r_scbond_it 2.805 r_mcangle_it 2.042 r_angle_refined_deg 1.552 r_symmetry_hbond_refined 1.348 r_mcbond_it 1.132 r_angle_other_deg 0.858 r_nbd_other 0.259 r_symmetry_vdw_other 0.239
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.95 r_scangle_it 4.474 r_scbond_it 2.805 r_mcangle_it 2.042 r_angle_refined_deg 1.552 r_symmetry_hbond_refined 1.348 r_mcbond_it 1.132 r_angle_other_deg 0.858 r_nbd_other 0.259 r_symmetry_vdw_other 0.239 r_nbd_refined 0.228 r_xyhbond_nbd_refined 0.186 r_symmetry_vdw_refined 0.159 r_chiral_restr 0.116 r_nbtor_other 0.1 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 6660 Nucleic Acid Atoms Solvent Atoms 236 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling EPMR phasing