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Crystal structure of a putative AphA-like transcription factor (ZP_00208345.1) from Magnetospirillum magnetotacticum MS-1 at 2.00 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 NANODROP, 15.0% Glycerol, 0.17M NaOAc, 25.5% PEG 4000, 0.1M Tris-HCl pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.55 51.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.62 α = 90 b = 66.62 β = 90 c = 92.6 γ = 90
Symmetry Space Group P 43 21 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 ADSC QUANTUM 315 2007-09-15 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.0000, 0.9795, 0.9797 ALS 8.2.1
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 2 28.364 99.7 0.046 16.26 14688 -3 44.566
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 2.07 97.4 0.665 2
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 28.364 14640 736 99.79 0.214 0.212 0.2147 0.256 0.2523 RANDOM 39.306
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] -0.27 -0.27 0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.38 r_dihedral_angle_4_deg 13.118 r_dihedral_angle_3_deg 10.605 r_scangle_it 5.758 r_scbond_it 4.326 r_dihedral_angle_1_deg 3.608 r_mcangle_it 2.621 r_mcbond_it 2.035 r_angle_refined_deg 1.456 r_angle_other_deg 1.341
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.38 r_dihedral_angle_4_deg 13.118 r_dihedral_angle_3_deg 10.605 r_scangle_it 5.758 r_scbond_it 4.326 r_dihedral_angle_1_deg 3.608 r_mcangle_it 2.621 r_mcbond_it 2.035 r_angle_refined_deg 1.456 r_angle_other_deg 1.341 r_mcbond_other 0.392 r_nbd_refined 0.187 r_symmetry_vdw_other 0.175 r_nbtor_refined 0.139 r_symmetry_vdw_refined 0.131 r_nbd_other 0.125 r_xyhbond_nbd_refined 0.1 r_chiral_restr 0.08 r_nbtor_other 0.074 r_symmetry_hbond_refined 0.062 r_bond_refined_d 0.014 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 1211 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms
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 SHELXD phasing SHARP phasing