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CRYSTAL STRUCTURE OF A CUPIN SUPERFAMILY PROTEIN (DSY2733) FROM DESULFITOBACTERIUM HAFNIENSE DCB-2 AT 1.60 A RESOLUTION
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 NANODROP, 0.25M Sodium chloride, 33.0% 2-methyl-2,4-pentanediol, 0.1M Tris-HCl pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.07 40.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.93 α = 90 b = 69.79 β = 90 c = 150.52 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) 2007-01-06 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837, 0.97941, 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 28.88 99.3 0.045 14.16 7.2 28987 22.8
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 1.6 1.66 97.3 97.3 0.675 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 1.6 28.88 28943 1475 99.53 0.18374 0.1822 0.1853 0.21269 0.2178 RANDOM 15.049
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 1.37 -1.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.489 r_dihedral_angle_4_deg 21.374 r_dihedral_angle_3_deg 14.455 r_dihedral_angle_1_deg 8.183 r_scangle_it 7.412 r_scbond_it 5.047 r_mcangle_it 3.137 r_mcbond_it 2.3 r_angle_refined_deg 1.748 r_angle_other_deg 0.966
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.489 r_dihedral_angle_4_deg 21.374 r_dihedral_angle_3_deg 14.455 r_dihedral_angle_1_deg 8.183 r_scangle_it 7.412 r_scbond_it 5.047 r_mcangle_it 3.137 r_mcbond_it 2.3 r_angle_refined_deg 1.748 r_angle_other_deg 0.966 r_mcbond_other 0.739 r_symmetry_vdw_other 0.292 r_symmetry_vdw_refined 0.283 r_nbd_refined 0.217 r_nbd_other 0.203 r_xyhbond_nbd_refined 0.176 r_nbtor_refined 0.169 r_symmetry_hbond_refined 0.132 r_chiral_restr 0.093 r_nbtor_other 0.089 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_xyhbond_nbd_other 0.002 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1674 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 6
Software Software Software Name Purpose MolProbity model building REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction MAR345 data collection XDS data reduction SHARP phasing