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Crystal structure of a pyridoxamine 5'-phosphate oxidase related protein (psyc_0186) from psychrobacter arcticus 273-4 at 2.50 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 NANODROP, 3.2M (NH4)2SO4, 0.1M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.39 63.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.063 α = 90 b = 106.063 β = 90 c = 87.218 γ = 90
Symmetry Space Group I 41 2 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 MARMOSAIC 300 mm CCD Adjustable focusing mirrors in K-B geometry 2007-08-20 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.95372, 0.97942 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.5 28.433 99.9 0.09 0.09 4.2 7.2 8894 75.19
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.56 100 0.01 1.046 0.7 7.4 636
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 2.5 28.433 8885 424 99.9 0.192 0.191 0.1925 0.226 0.2351 RANDOM 42.729
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] -1.76 -1.76 3.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.902 r_dihedral_angle_4_deg 18.761 r_dihedral_angle_3_deg 17.239 r_scangle_it 7.797 r_dihedral_angle_1_deg 7.696 r_scbond_it 5.367 r_mcangle_it 3.094 r_mcbond_it 1.941 r_angle_refined_deg 1.645 r_angle_other_deg 1.123
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.902 r_dihedral_angle_4_deg 18.761 r_dihedral_angle_3_deg 17.239 r_scangle_it 7.797 r_dihedral_angle_1_deg 7.696 r_scbond_it 5.367 r_mcangle_it 3.094 r_mcbond_it 1.941 r_angle_refined_deg 1.645 r_angle_other_deg 1.123 r_mcbond_other 0.37 r_nbd_refined 0.201 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.167 r_symmetry_vdw_refined 0.167 r_nbd_other 0.162 r_symmetry_hbond_refined 0.161 r_symmetry_vdw_other 0.16 r_chiral_restr 0.094 r_nbtor_other 0.093 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1019 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction SHELXD phasing