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Crystal structure of DapB in complex with NADP+ from Corynebacterium glutamicum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EER
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.75 293 Ammonium sulfate, Sodium acetate trihydrate
Crystal Properties Matthews coefficient Solvent content 4.84 74.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.969 α = 90 b = 107.969 β = 90 c = 172.049 γ = 90
Symmetry Space Group I 41 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 270 2014-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97934 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.14 50 95.1 8.6 8.6 25394
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.14 2.18 85.4 3
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 5EER 2.15 50 25394 1364 95.08 0.1803 0.1786 0.1925 0.2112 0.2196 RANDOM 52.835
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] 0.84 0.84 -1.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.398 r_dihedral_angle_4_deg 19.538 r_dihedral_angle_3_deg 15.359 r_dihedral_angle_1_deg 7.841 r_mcangle_it 6.089 r_mcbond_it 4.292 r_mcbond_other 4.257 r_angle_refined_deg 2.203 r_angle_other_deg 1.093 r_chiral_restr 0.108
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.398 r_dihedral_angle_4_deg 19.538 r_dihedral_angle_3_deg 15.359 r_dihedral_angle_1_deg 7.841 r_mcangle_it 6.089 r_mcbond_it 4.292 r_mcbond_other 4.257 r_angle_refined_deg 2.203 r_angle_other_deg 1.093 r_chiral_restr 0.108 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1820 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 64
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling CNS phasing