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CRYSTAL STRUCTURE OF A PUTATIVE PYRIDOXAMINE 5'-PHOSPHATE OXIDASE (LDB0262) FROM LACTOBACILLUS DELBRUECKII SUBSP. AT 1.60 A RESOLUTION
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4 277 2.4M (NH4)2SO4, 0.1M Citrate pH 4.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.89 34.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.104 α = 90 b = 71.123 β = 90.86 c = 47.031 γ = 90
Symmetry Space Group P 1 21 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 collimating mirror, toroid focusing mirror 2006-07-02 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837,0.97929,0.97911 SSRL BL9-2
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 1.595 39.253 99.9 0.107 0.107 4.8 5.2 29681
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 1.6 1.68 99.8 0.987 0.987 0.7 3.6 4059
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 1.6 39.253 29659 1486 99.79 0.16 0.158 0.1693 0.206 0.2126 RANDOM 12.657
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] -0.6 0.14 2.28 -1.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.097 r_dihedral_angle_4_deg 13.413 r_dihedral_angle_3_deg 12.389 r_scangle_it 6.49 r_dihedral_angle_1_deg 6.222 r_scbond_it 4.972 r_mcangle_it 2.788 r_mcbond_it 1.954 r_angle_refined_deg 1.566 r_angle_other_deg 0.873
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.097 r_dihedral_angle_4_deg 13.413 r_dihedral_angle_3_deg 12.389 r_scangle_it 6.49 r_dihedral_angle_1_deg 6.222 r_scbond_it 4.972 r_mcangle_it 2.788 r_mcbond_it 1.954 r_angle_refined_deg 1.566 r_angle_other_deg 0.873 r_mcbond_other 0.792 r_symmetry_vdw_refined 0.224 r_nbd_refined 0.216 r_symmetry_vdw_other 0.204 r_nbd_other 0.188 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.158 r_symmetry_hbond_refined 0.153 r_chiral_restr 0.088 r_nbtor_other 0.087 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1874 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 31
Software Software Software Name Purpose MolProbity model building SHELX phasing REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling SHELXD phasing autoSHARP phasing