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Crystal structure of the catalytically active form of diaminopimelate epimerase from Bacillus anthracis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GQZ PDB ENTRY 1GQZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.6 293 0.2 M ammonium formate, 20% PEG 3350, 3% ethylene glycol, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 6.60
Crystal Properties Matthews coefficient Solvent content 2.31 46.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.863 α = 90 b = 87.334 β = 90 c = 110.453 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 IMAGE PLATE RIGAKU RAXIS IV 2005-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
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 2.4 50 98.9 0.074 23.6 6.7 24966 -4 54
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 2.4 2.49 0.488 3.1
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 PDB ENTRY 1GQZ 2.4 36.23 23674 1234 98.9 0.184 0.18 0.1829 0.25 0.2525 RANDOM 25.879
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] -1.67 0.51 1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.73 r_dihedral_angle_3_deg 16.215 r_dihedral_angle_4_deg 14.402 r_scangle_it 6.75 r_dihedral_angle_1_deg 6.722 r_scbond_it 5.469 r_mcangle_it 4.193 r_mcbond_it 3.497 r_angle_refined_deg 1.329 r_angle_other_deg 1.145
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.73 r_dihedral_angle_3_deg 16.215 r_dihedral_angle_4_deg 14.402 r_scangle_it 6.75 r_dihedral_angle_1_deg 6.722 r_scbond_it 5.469 r_mcangle_it 4.193 r_mcbond_it 3.497 r_angle_refined_deg 1.329 r_angle_other_deg 1.145 r_mcbond_other 0.874 r_symmetry_vdw_other 0.241 r_symmetry_hbond_refined 0.209 r_nbd_other 0.198 r_nbd_refined 0.182 r_xyhbond_nbd_refined 0.181 r_nbtor_refined 0.17 r_symmetry_vdw_refined 0.131 r_nbtor_other 0.086 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4470 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing