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Crystal structure of a cupin-2 domain containing protein (sfri_3543) from shewanella frigidimarina ncimb 400 at 2.05 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.9 293 0.2000M K2NO3, 20.0000% PEG-3350, No Buffer pH 6., NANODROP, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.62 52.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.92 α = 90 b = 95.14 β = 90 c = 237.37 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 collimating mirror, toroid focusing mirror 2008-03-16 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837,0.97929,0.97918 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 2.05 27.853 97 0.04 11.7 40296 -3 36.405
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 2.05 2.12 83.7 0.35 1.9
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 2.05 27.853 40280 2018 98.65 0.187 0.186 0.1938 0.212 0.2216 RANDOM 44.746
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] 0.22 -1.93 1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.085 r_dihedral_angle_3_deg 11.805 r_dihedral_angle_4_deg 9.108 r_scangle_it 4.77 r_dihedral_angle_1_deg 4.104 r_scbond_it 3.506 r_mcangle_it 1.833 r_angle_refined_deg 1.632 r_angle_other_deg 1.23 r_mcbond_it 1.132
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.085 r_dihedral_angle_3_deg 11.805 r_dihedral_angle_4_deg 9.108 r_scangle_it 4.77 r_dihedral_angle_1_deg 4.104 r_scbond_it 3.506 r_mcangle_it 1.833 r_angle_refined_deg 1.632 r_angle_other_deg 1.23 r_mcbond_it 1.132 r_mcbond_other 0.232 r_symmetry_vdw_other 0.175 r_nbd_refined 0.168 r_nbtor_refined 0.162 r_nbd_other 0.142 r_symmetry_vdw_refined 0.123 r_chiral_restr 0.102 r_symmetry_hbond_refined 0.091 r_xyhbond_nbd_refined 0.09 r_nbtor_other 0.072 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4170 Nucleic Acid Atoms Solvent Atoms 237 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing