☰ Navigation Tabs
4-hydroxy tetrahydrodipicolinate reductase from Neisseria gonorrhoeae
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 6.5 298 0.1 M BIS-TRIS pH 6.5, 2.0 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.53 51.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.803 α = 90 b = 71.723 β = 90 c = 138.414 γ = 90
Symmetry Space Group I 2 2 2
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 210r 2016-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.85 40 99.9 0.061 0.061 0.067 0.024 48.2 7.9 25492 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.88 100 0.784 0.784 0.757 0.27 3.38 7.8
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 1.85 40 23783 1173 99.83 0.17139 0.16943 0.1822 0.20989 0.2215 RANDOM 38.09
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] 2.3 -0.67 -1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.505 r_dihedral_angle_4_deg 20.908 r_dihedral_angle_3_deg 12.181 r_long_range_B_refined 7.109 r_long_range_B_other 6.968 r_dihedral_angle_1_deg 5.936 r_scangle_other 5.203 r_scbond_it 3.844 r_angle_other_deg 3.833 r_scbond_other 3.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.505 r_dihedral_angle_4_deg 20.908 r_dihedral_angle_3_deg 12.181 r_long_range_B_refined 7.109 r_long_range_B_other 6.968 r_dihedral_angle_1_deg 5.936 r_scangle_other 5.203 r_scbond_it 3.844 r_angle_other_deg 3.833 r_scbond_other 3.321 r_mcangle_it 3.259 r_mcangle_other 3.258 r_mcbond_it 2.338 r_mcbond_other 2.338 r_angle_refined_deg 1.911 r_chiral_restr 0.133 r_bond_refined_d 0.021 r_gen_planes_other 0.01 r_gen_planes_refined 0.009 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1885 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling MOLREP phasing HKL-3000 refinement