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Crystal structure of a dabb family protein with a ferredoxin-like fold (mll5499) from mesorhizobium loti maff303099 at 1.79 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.9 277 NANODROP, 0.2M Na Acetate, 20.0% PEG 3350, No Buffer pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2 38.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.669 α = 90 b = 28.415 β = 117.78 c = 76.985 γ = 90
Symmetry Space Group C 1 2 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 KOHZU: Double crystal Si(111) 2007-10-04 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 0.9537, 0.9797, 0.9796 ALS 8.2.2
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 1.79 29.54 94.5 0.074 0.074 7.8 2.3 20638 18.85
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 1.79 1.84 73.2 0.465 0.465 1.7 1.6 1153
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 1.79 29.54 20637 1063 94.02 0.179 0.177 0.1853 0.224 0.2368 RANDOM 16.841
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] -0.24 -0.51 0.38 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.502 r_dihedral_angle_4_deg 26.582 r_dihedral_angle_3_deg 10.166 r_scangle_it 5.631 r_scbond_it 4.36 r_dihedral_angle_1_deg 4.245 r_mcangle_it 2.547 r_mcbond_it 1.935 r_angle_refined_deg 1.62 r_angle_other_deg 1.269
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.502 r_dihedral_angle_4_deg 26.582 r_dihedral_angle_3_deg 10.166 r_scangle_it 5.631 r_scbond_it 4.36 r_dihedral_angle_1_deg 4.245 r_mcangle_it 2.547 r_mcbond_it 1.935 r_angle_refined_deg 1.62 r_angle_other_deg 1.269 r_mcbond_other 0.447 r_symmetry_vdw_other 0.193 r_nbd_refined 0.178 r_nbtor_refined 0.166 r_symmetry_vdw_refined 0.156 r_nbd_other 0.145 r_xyhbond_nbd_refined 0.102 r_symmetry_hbond_refined 0.093 r_chiral_restr 0.088 r_nbtor_other 0.075 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1640 Nucleic Acid Atoms Solvent Atoms 253 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction SHELXD phasing SHARP phasing