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Crystal Structure of the Nitroreductase CinD from Lactococcus lactis in Complex with FMN
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IFA PDB ENTRY 2IFA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.2M MGCL2, 0.1M TRISHCL PH 8.0, 5% MPD (V/V), 20% PEG 3350 (W/V), 1MM FMN, 4MM DTT
Crystal Properties Matthews coefficient Solvent content 2.47 50.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.843 α = 90 b = 120.147 β = 90 c = 68.659 γ = 90
Symmetry Space Group C 2 2 21
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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA SLS X06DA
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 1.35 49.15 99.2 0.09 12.36 8.9 48865 -3
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 1.35 1.4 97.3 0.58 1.9
Refinement Statistics Diffraction ID Structure Solution 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 PDB ENTRY 2IFA 1.35 32.134 2 48850 1466 99.21 0.1322 0.1315 0.132 0.1555 0.1591
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] -0.0209 -0.198 0.2188
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.589 f_angle_d 0.863 f_chiral_restr 0.069 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1469 Nucleic Acid Atoms Solvent Atoms 296 Heterogen Atoms 31
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing