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Crystal structure of dihydrodipicolinate synthase from the pathogen Neisseria meningitidis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YXC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.3 291 1.8M ammonium sulfate, 100mM Bis-Tris.HCl, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.44 49.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.667 α = 90 b = 115.684 β = 90 c = 132.122 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 315 2008-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9796 Diamond I02
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 1.999 115.684 99.9 0.096 5.7 84335 84251 21.23
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 2.07 100 0.349 5.7 8359
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1YXC 2 115.47 84324 84214 4201 99.87 0.151 0.148 0.1503 0.191 0.1923 RANDOM 20.562
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] 0.34 -0.7 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.065 r_dihedral_angle_4_deg 16.803 r_dihedral_angle_3_deg 12.642 r_dihedral_angle_1_deg 6.825 r_scangle_it 6.212 r_scbond_it 4.421 r_mcangle_it 2.259 r_mcbond_it 1.726 r_angle_refined_deg 1.133 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.065 r_dihedral_angle_4_deg 16.803 r_dihedral_angle_3_deg 12.642 r_dihedral_angle_1_deg 6.825 r_scangle_it 6.212 r_scbond_it 4.421 r_mcangle_it 2.259 r_mcbond_it 1.726 r_angle_refined_deg 1.133 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.242 r_nbd_refined 0.213 r_symmetry_hbond_refined 0.179 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.09 r_gen_planes_refined 0.012 r_bond_refined_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8722 Nucleic Acid Atoms Solvent Atoms 938 Heterogen Atoms 264
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction DNA data collection DENZO data reduction SCALEPACK data scaling