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Crystal Structure of Pseudomonas aeruginosa D-Arginine Dehydrogenase in Complex with an (N5) Flavin Adduct
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NYE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 277 Crystals were grown by the hanging drop vapor diffusion method using a well solution of 0.1M 2-(N-morpholino)-ethanesulfonic acid (MES) pH 6.5-7.0, 5% glycerol, and 6-10% (w/v) PEG6000., VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.61 52.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.072 α = 90 b = 77.933 β = 90 c = 89.31 γ = 90
Symmetry Space Group P 21 21 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 300 mm CCD 2010-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.80000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.07 50 98.6 0.067 10.8 187536
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 1.07 1.09 80.8 0.438 2.3 3.8 7585
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 FREE R PDB entry 3YNE 1.07 10 187151 9363 98.4 0.1446 0.1446 0.1329 0.1654 0.151 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 25 3323.12
RMS Deviations Key Refinement Restraint Deviation s_zero_chiral_vol 0.094 s_non_zero_chiral_vol 0.093 s_similar_adp_cmpnt 0.053 s_anti_bump_dis_restr 0.052 s_angle_d 0.033 s_from_restr_planes 0.0306 s_bond_d 0.016 s_rigid_bond_adp_cmpnt 0.007 s_similar_dist s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2917 Nucleic Acid Atoms Solvent Atoms 349 Heterogen Atoms 77
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing SHELXL-97 refinement HKL-2000 data reduction HKL-2000 data scaling