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CRYSTAL STRUCTURE OF a DUF849 family protein (PDEN_3495) FROM PARACOCCUS DENITRIFICANS PD1222 AT 1.90 A RESOLUTION
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.314M magnesium chloride, 20.4% polyethylene glycol 3350, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.38 48.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.579 α = 90 b = 139.567 β = 90 c = 45.765 γ = 90
Symmetry Space Group P 21 21 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 2008-10-12 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.94645,0.97967 APS 23-ID-B
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 1.9 29.501 90.8 0.136 0.136 4.467 5.2 43418 17.226
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 1.9 1.95 82.2 0.521 0.521 1.5 2.9 2851
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 1.9 29.501 43231 2222 90.3 0.207 0.205 0.2083 0.248 0.2504 RANDOM 22.746
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] -1.18 -3.08 4.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.331 r_dihedral_angle_4_deg 19.498 r_dihedral_angle_3_deg 13.618 r_scangle_it 6.778 r_dihedral_angle_1_deg 5.876 r_scbond_it 5.135 r_mcangle_it 2.72 r_mcbond_it 1.818 r_angle_refined_deg 1.538 r_angle_other_deg 0.936
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.331 r_dihedral_angle_4_deg 19.498 r_dihedral_angle_3_deg 13.618 r_scangle_it 6.778 r_dihedral_angle_1_deg 5.876 r_scbond_it 5.135 r_mcangle_it 2.72 r_mcbond_it 1.818 r_angle_refined_deg 1.538 r_angle_other_deg 0.936 r_mcbond_other 0.727 r_chiral_restr 0.089 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4194 Nucleic Acid Atoms Solvent Atoms 421 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction SHELXD phasing autoSHARP phasing