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Crystal Structure of a Rex-family transcriptional regulatory protein from Streptococcus agalactiae complexed with NAD+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DT5 PDB ENTRY 2DT5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 20% PEG 6000, 175mM magnesium chloride, 100mM HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.11 41.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.27 α = 90 b = 92.41 β = 91.26 c = 47.19 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 MAR CCD 165 mm mirrors 2009-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 1.0379 MAX II I911-2
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 1.5 27.1 98 0.084 8.42 3.6 63360 62064 -3
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) 1.5 1.54 93.3 0.528 2.26 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2DT5 1.5 27.07 58774 3147 97.62 0.17845 0.17544 0.1897 0.23436 0.2447 RANDOM 11.49
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] -0.05 0.04 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.295 r_dihedral_angle_4_deg 21.74 r_dihedral_angle_3_deg 13.137 r_sphericity_free 10.687 r_scangle_it 6.375 r_dihedral_angle_1_deg 5.406 r_scbond_it 4.639 r_sphericity_bonded 4.262 r_mcangle_it 3.176 r_rigid_bond_restr 2.268
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.295 r_dihedral_angle_4_deg 21.74 r_dihedral_angle_3_deg 13.137 r_sphericity_free 10.687 r_scangle_it 6.375 r_dihedral_angle_1_deg 5.406 r_scbond_it 4.639 r_sphericity_bonded 4.262 r_mcangle_it 3.176 r_rigid_bond_restr 2.268 r_mcbond_it 2.19 r_angle_refined_deg 2.038 r_angle_other_deg 1.101 r_mcbond_other 0.944 r_chiral_restr 0.137 r_bond_refined_d 0.025 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3258 Nucleic Acid Atoms Solvent Atoms 544 Heterogen Atoms 96
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling