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Crystal structure of a rmlc-like cupin protein (dde_2303) from desulfovibrio desulfuricans subsp. at 1.94 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 NANODROP, 35.0% PEG 3000, 0.2M Sodium chloride, 0.1M Tris-HCl pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K 2 VAPOR DIFFUSION, SITTING DROP 8 293 NANODROP, 40.0% PEG 3000, 0.2M Sodium chloride, 0.1M Tris-HCl pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.14 α = 90 b = 133.95 β = 93.04 c = 74.66 γ = 90
Symmetry Space Group P 1 21 1
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 ADSC QUANTUM 315 2006-09-10 M SINGLE WAVELENGTH 2 2 x-ray 100 CCD ADSC QUANTUM 315 Vertically collimating premirror, toroidal focusing hexapod mirror 2006-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 1.00000 ALS 5.0.3 2 SYNCHROTRON ALS BEAMLINE 5.0.2 0.98030 ALS 5.0.2
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 1.94 29.025 81.5 0.06 8.45 60310 -3 29.144
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 1.94 2.01 57 0.317 2.5
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 SAD THROUGHOUT 1.94 29.025 60283 3173 96.41 0.169 0.167 0.175 0.212 0.2176 RANDOM 26.755
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] 0.16 0.8 -2.05 1.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.767 r_dihedral_angle_4_deg 17.609 r_dihedral_angle_3_deg 10.34 r_scangle_it 6.636 r_scbond_it 4.724 r_dihedral_angle_1_deg 4.561 r_mcangle_it 2.306 r_mcbond_it 1.951 r_angle_refined_deg 1.791 r_angle_other_deg 1.288
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.767 r_dihedral_angle_4_deg 17.609 r_dihedral_angle_3_deg 10.34 r_scangle_it 6.636 r_scbond_it 4.724 r_dihedral_angle_1_deg 4.561 r_mcangle_it 2.306 r_mcbond_it 1.951 r_angle_refined_deg 1.791 r_angle_other_deg 1.288 r_mcbond_other 0.584 r_nbd_refined 0.16 r_nbtor_refined 0.153 r_symmetry_vdw_other 0.151 r_nbd_other 0.149 r_symmetry_hbond_refined 0.116 r_symmetry_vdw_refined 0.108 r_chiral_restr 0.105 r_xyhbond_nbd_refined 0.105 r_nbtor_other 0.077 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.005 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6366 Nucleic Acid Atoms Solvent Atoms 654 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction ADSC data collection XDS data reduction SHARP phasing