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Crystal structure of NADP-dependent carbonyl reductase from Burkholderia multivorans in complex with NADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IDQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 MORPHEUS A10: 10% w/v PEG 8000, 20% v/v EG, 30mM MgCl2, 20mM, CaCl2, 100mM bicene/Trizma base pH 8.5, 4mM NADP; protein conc. 23.4mg/mL, direct cryo, puck/pin gdy5-3
Crystal Properties Matthews coefficient Solvent content 2.45 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.34 α = 90 b = 90.31 β = 90 c = 50.91 γ = 90
Symmetry Space Group P 21 21 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 RAYONIX MX-300 2016-07-05 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.9 50 99.2 0.05 0.999 23.01 6.1 19862 -3 26.89
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.95 100 0.539 0.884 3.52 8920
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5idq 1.9 28.539 1.34 19853 2058 99.15 0.1531 0.149 0.1498 0.1881 0.1871 31.0236
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.093 f_angle_d 0.827 f_chiral_restr 0.052 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1671 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 52
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing PHENIX refinement PDB_EXTRACT data extraction Coot model building XDS data reduction