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Crystal structure of putative dinucleotide-binding oxidoreductase (NP_786167.1) from Lactobacillus plantarum at 1.60 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 NANODROP, 20.0% PEG 3350, 0.2M Ammonium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.06 40.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.33 α = 90 b = 152.57 β = 90 c = 140.07 γ = 90
Symmetry Space Group C 2 2 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 325 mm CCD Flat mirror (vertical focusing) 2007-07-25 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837, 0.97886, 0.97917 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 1.6 29.54 99.2 0.053 10.8 75349 -3 20.872
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) 1.6 1.66 98.5 0.368 2.2
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 1.6 29.54 75306 3791 99.59 0.153 0.151 0.1582 0.186 0.1921 RANDOM 11.56
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] 0.29 -0.14 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.163 r_dihedral_angle_3_deg 10.461 r_dihedral_angle_4_deg 7.544 r_scangle_it 6.387 r_dihedral_angle_1_deg 4.599 r_scbond_it 4.512 r_mcangle_it 2.789 r_mcbond_it 2.227 r_angle_refined_deg 1.751 r_angle_other_deg 1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.163 r_dihedral_angle_3_deg 10.461 r_dihedral_angle_4_deg 7.544 r_scangle_it 6.387 r_dihedral_angle_1_deg 4.599 r_scbond_it 4.512 r_mcangle_it 2.789 r_mcbond_it 2.227 r_angle_refined_deg 1.751 r_angle_other_deg 1.42 r_mcbond_other 0.532 r_symmetry_vdw_other 0.239 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.198 r_nbtor_refined 0.175 r_symmetry_hbond_refined 0.175 r_nbd_other 0.157 r_xyhbond_nbd_refined 0.157 r_xyhbond_nbd_other 0.134 r_chiral_restr 0.086 r_nbtor_other 0.085 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4543 Nucleic Acid Atoms Solvent Atoms 626 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SOLVE phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction MAR345 data collection XDS data reduction