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Crystal structure of Dihydrodipicolinate reductase (TM1520) from Thermotoga maritima at 2.27 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ARZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 4.5 293 20.0% PEG-400, 0.2M Ca(OAc)2, 0.1M Acetate pH 4.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.38 63.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.077 α = 90 b = 109.217 β = 119.23 c = 112.602 γ = 90
Symmetry Space Group C 1 2 1
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 flat mirror 2004-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.27 29.03 47.8 0.086 10.8 3.6 61963 46.59
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.27 2.39 38.4 0.507 2 2.5 7228
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 1arz 2.27 29.03 58811 3151 95.49 0.17334 0.17127 0.1764 0.21256 0.2167 RANDOM 42.509
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] 1.77 -0.6 0.29 -2.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.816 r_dihedral_angle_4_deg 17.957 r_dihedral_angle_3_deg 14.438 r_dihedral_angle_1_deg 5.804 r_scangle_it 5.093 r_scbond_it 3.936 r_mcangle_it 1.742 r_angle_refined_deg 1.596 r_mcbond_it 1.237 r_angle_other_deg 0.919
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.816 r_dihedral_angle_4_deg 17.957 r_dihedral_angle_3_deg 14.438 r_dihedral_angle_1_deg 5.804 r_scangle_it 5.093 r_scbond_it 3.936 r_mcangle_it 1.742 r_angle_refined_deg 1.596 r_mcbond_it 1.237 r_angle_other_deg 0.919 r_mcbond_other 0.526 r_symmetry_vdw_other 0.205 r_nbd_refined 0.196 r_symmetry_vdw_refined 0.196 r_symmetry_hbond_refined 0.187 r_nbd_other 0.177 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.175 r_chiral_restr 0.089 r_nbtor_other 0.086 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6730 Nucleic Acid Atoms Solvent Atoms 529 Heterogen Atoms 275
Software Software Software Name Purpose XDS data scaling XSCALE data scaling SCALA data scaling MOLREP phasing REFMAC refinement XDS data reduction CCP4 data scaling