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Crystal Structure of Dihydrodipicolinate Synthase DapA-2 (BA3935) from Bacillus Anthracis at 1.94A Resolution.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DHP PDB ENTRY 1DHP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 PEG 5000 MME, KSCN, TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.4 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.203 α = 90 b = 126.882 β = 90 c = 173.319 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 120 IMAGE PLATE MARRESEARCH multilayer optics 2004-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54189
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 1.94 20 95.6 0.082 17.2 5.4 87118 87118 29.2
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) 1.94 2.01 84.7 0.315 3 3.4 7624
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 (All) 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 1DHP 1.94 19.96 87004 82644 4360 100 0.15555 0.15555 0.1534 0.1667 0.19719 0.2077 RANDOM 16.158
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] 0.03 -0.11 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.614 r_dihedral_angle_4_deg 14.395 r_dihedral_angle_3_deg 12.939 r_dihedral_angle_1_deg 5.642 r_scangle_it 2.67 r_scbond_it 1.532 r_angle_refined_deg 1.183 r_angle_other_deg 0.898 r_mcangle_it 0.839 r_mcbond_it 0.433
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.614 r_dihedral_angle_4_deg 14.395 r_dihedral_angle_3_deg 12.939 r_dihedral_angle_1_deg 5.642 r_scangle_it 2.67 r_scbond_it 1.532 r_angle_refined_deg 1.183 r_angle_other_deg 0.898 r_mcangle_it 0.839 r_mcbond_it 0.433 r_nbd_refined 0.229 r_symmetry_vdw_other 0.191 r_nbtor_refined 0.165 r_nbd_other 0.164 r_symmetry_vdw_refined 0.162 r_symmetry_hbond_refined 0.142 r_xyhbond_nbd_refined 0.132 r_metal_ion_refined 0.099 r_chiral_restr 0.095 r_mcbond_other 0.087 r_nbtor_other 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8758 Nucleic Acid Atoms Solvent Atoms 1748 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing