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NADPH complex structure of Aldehyde Dehydrogenase from Bacillus cereus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PS9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 287 0.15M DL MALIC ACID PH 7.0, 18% PEG
3350 (W/V)
Crystal Properties Matthews coefficient Solvent content 2.61 52.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.887 α = 90 b = 93.94 β = 97.67 c = 144.934 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 ADSC QUANTUM 315r 2013-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.99998 PAL/PLS 5C (4A)
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 50 99.9 0.079 42.8 7.3 149308
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 2.03 100 0.39 6.4
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 4PS9 2 47.88 142763 7525 99.85 0.19259 0.18949 0.2031 0.2518 0.2594 RANDOM 32.964
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] 0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.755 r_dihedral_angle_4_deg 20.339 r_dihedral_angle_3_deg 16.871 r_dihedral_angle_1_deg 7.344 r_long_range_B_refined 6.713 r_long_range_B_other 6.696 r_scangle_other 5.146 r_mcangle_it 3.537 r_mcangle_other 3.537 r_scbond_it 3.398
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.755 r_dihedral_angle_4_deg 20.339 r_dihedral_angle_3_deg 16.871 r_dihedral_angle_1_deg 7.344 r_long_range_B_refined 6.713 r_long_range_B_other 6.696 r_scangle_other 5.146 r_mcangle_it 3.537 r_mcangle_other 3.537 r_scbond_it 3.398 r_scbond_other 3.398 r_mcbond_it 2.631 r_mcbond_other 2.631 r_angle_refined_deg 1.903 r_angle_other_deg 1.084 r_chiral_restr 0.126 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 15126 Nucleic Acid Atoms Solvent Atoms 1499 Heterogen Atoms 199
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASES phasing