☰ Navigation Tabs
Crystal structure of Putative pyridoxamine 5'-phosphate oxidase (NP_601736.1) from CORYNEBACTERIUM GLUTAMICUM ATCC 13032 KITASATO at 2.51 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 0.2000M Ca(OAc)2, 20.0000% PEG-8000, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.37 48.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.63 α = 90 b = 88.31 β = 90 c = 138.17 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 Adjustable focusing mirrors in K-B geometry 2008-10-13 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.94645,0.97962 APS 23-ID-B
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 2.51 29.54 96 0.062 15.98 31540 -3 52.655
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 2.5 2.59 69.8 0.296 2
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 2.51 29.54 31509 1601 98.24 0.245 0.243 0.2436 0.287 0.2905 RANDOM 52.455
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] 1.72 -1.65 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.043 r_dihedral_angle_3_deg 11.856 r_dihedral_angle_4_deg 11.827 r_scangle_it 5.743 r_scbond_it 4.087 r_dihedral_angle_1_deg 3.742 r_mcangle_it 2.249 r_angle_refined_deg 1.647 r_mcbond_it 1.292 r_angle_other_deg 1.272
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.043 r_dihedral_angle_3_deg 11.856 r_dihedral_angle_4_deg 11.827 r_scangle_it 5.743 r_scbond_it 4.087 r_dihedral_angle_1_deg 3.742 r_mcangle_it 2.249 r_angle_refined_deg 1.647 r_mcbond_it 1.292 r_angle_other_deg 1.272 r_mcbond_other 0.459 r_symmetry_vdw_other 0.161 r_nbtor_refined 0.149 r_nbd_refined 0.148 r_nbd_other 0.139 r_symmetry_hbond_refined 0.133 r_symmetry_vdw_refined 0.118 r_xyhbond_nbd_refined 0.107 r_chiral_restr 0.09 r_nbtor_other 0.068 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6028 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 70
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