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Crystal structure of protein with a cupin-like fold and unknown function (YP_001165807.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.91 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.9 277 0.2M NaThioCyanate, 20.0% PEG-3350, No Buffer pH 6.9, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.51 50.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.33 α = 90 b = 78.33 β = 90 c = 107.32 γ = 120
Symmetry Space Group P 64 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 325 mm CCD Flat collimating mirror, toroid focusing mirror 2008-08-11 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.92522,0.97932,0.97879 SSRL BL9-2
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 1.91 28.665 98 0.147 13.43 15326 -3 22.05
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 1.91 1.98 97.4 0.011 2.1
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 1.91 28.665 15326 765 97.54 0.172 0.17 0.1735 0.205 0.21 RANDOM 22.97
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] 0.96 0.48 0.96 -1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.891 r_dihedral_angle_4_deg 18.022 r_dihedral_angle_3_deg 13.223 r_dihedral_angle_1_deg 6.995 r_scangle_it 3.084 r_scbond_it 2.097 r_angle_refined_deg 1.571 r_angle_other_deg 1.413 r_mcangle_it 1.323 r_mcbond_it 0.815
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.891 r_dihedral_angle_4_deg 18.022 r_dihedral_angle_3_deg 13.223 r_dihedral_angle_1_deg 6.995 r_scangle_it 3.084 r_scbond_it 2.097 r_angle_refined_deg 1.571 r_angle_other_deg 1.413 r_mcangle_it 1.323 r_mcbond_it 0.815 r_mcbond_other 0.226 r_chiral_restr 0.089 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1237 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHARP phasing