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Crystal structure of Putative Pyridoxamine 5'-phosphate oxidase (NP_472219.1) from LISTERIA INNOCUA at 2.00 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.57 277 40.9% 1,2-propanediol, 0.1M sodium acetate pH 4.57, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.07 40.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.16 α = 90 b = 42.23 β = 91.59 c = 62.02 γ = 90
Symmetry Space Group C 1 2 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 325 mm CCD Flat mirror (vertical focusing) 2008-04-13 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97956,0.97908 SSRL BL11-1
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 26.055 98.1 0.063 8.88 3.7 16307 -3 26.246
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 2.07 92.9 0.459 1.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2 26.055 16307 828 99.58 0.185 0.182 0.1857 0.239 0.2403 RANDOM 23.25
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] 0.04 -1.27 0.32 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.051 r_dihedral_angle_4_deg 14.793 r_dihedral_angle_3_deg 12.326 r_scangle_it 8.194 r_scbond_it 5.578 r_dihedral_angle_1_deg 3.978 r_mcangle_it 3.193 r_mcbond_it 1.942 r_angle_refined_deg 1.725 r_angle_other_deg 1.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.051 r_dihedral_angle_4_deg 14.793 r_dihedral_angle_3_deg 12.326 r_scangle_it 8.194 r_scbond_it 5.578 r_dihedral_angle_1_deg 3.978 r_mcangle_it 3.193 r_mcbond_it 1.942 r_angle_refined_deg 1.725 r_angle_other_deg 1.005 r_mcbond_other 0.725 r_chiral_restr 0.099 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1863 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing