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Pseudomonas aeruginosa DapD (PA3666) apoprotein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3R5C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 293 19-20% of PEG3350, 0.3-0.4M succinate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.62 53.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.038 α = 90 b = 102.002 β = 89.97 c = 134.903 γ = 90
Symmetry Space Group P 1 21 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 MARMOSAIC 225 mm CCD 2009-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 1.000 MAX II I911-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.8 25.06 91.8 0.057 0.057 10.8 2.6 190821 190821
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 62.7 0.37 0.37 2.8 1.9
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 (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 3R5C 1.8 24.38 181087 181087 9659 91.61 0.20332 0.20156 0.2085 0.23639 0.2375 RANDOM 20.338
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 -0.5 -0.19 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.483 r_dihedral_angle_4_deg 21.859 r_dihedral_angle_3_deg 13.951 r_dihedral_angle_1_deg 5.772 r_scangle_it 1.468 r_angle_refined_deg 1.086 r_scbond_it 0.925 r_angle_other_deg 0.838 r_mcangle_it 0.654 r_mcbond_it 0.368
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.483 r_dihedral_angle_4_deg 21.859 r_dihedral_angle_3_deg 13.951 r_dihedral_angle_1_deg 5.772 r_scangle_it 1.468 r_angle_refined_deg 1.086 r_scbond_it 0.925 r_angle_other_deg 0.838 r_mcangle_it 0.654 r_mcbond_it 0.368 r_mcbond_other 0.109 r_chiral_restr 0.061 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14144 Nucleic Acid Atoms Solvent Atoms 705 Heterogen Atoms 12
Software Software Software Name Purpose MxCuBE data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling