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Crystal structure of Pyridoxamine 5'-phosphate oxidase-like protein (NP_783940.1) from Lactobacillus plantarum at 1.55 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 NANODROP, 2.0M (NH4)2SO4, 0.2M Li2SO4, 0.1M Tris-HCl pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.33 63.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.379 α = 90 b = 137.379 β = 90 c = 137.379 γ = 90
Symmetry Space Group P 43 3 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 ADSC QUANTUM 315 2007-09-17 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.0000, 0.9797 ALS 8.2.1
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 1.55 29.975 100 0.083 0.083 5.4 10.1 64534 19.3
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 1.55 1.59 100 0.913 0.913 0.9 9.2 4687
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 1.55 29.975 64447 3263 99.97 0.171 0.17 0.1761 0.196 0.2033 RANDOM 16.142
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.986 r_dihedral_angle_4_deg 22.262 r_dihedral_angle_3_deg 12.127 r_dihedral_angle_1_deg 6.643 r_scangle_it 6.065 r_scbond_it 4.472 r_mcangle_it 2.894 r_mcbond_it 2.274 r_angle_refined_deg 1.684 r_angle_other_deg 0.987
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.986 r_dihedral_angle_4_deg 22.262 r_dihedral_angle_3_deg 12.127 r_dihedral_angle_1_deg 6.643 r_scangle_it 6.065 r_scbond_it 4.472 r_mcangle_it 2.894 r_mcbond_it 2.274 r_angle_refined_deg 1.684 r_angle_other_deg 0.987 r_mcbond_other 0.595 r_symmetry_vdw_refined 0.27 r_symmetry_hbond_refined 0.246 r_nbd_refined 0.244 r_symmetry_vdw_other 0.2 r_nbd_other 0.197 r_xyhbond_nbd_refined 0.179 r_nbtor_refined 0.175 r_chiral_restr 0.101 r_nbtor_other 0.088 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2228 Nucleic Acid Atoms Solvent Atoms 413 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SOLVE phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction