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Crystal structure of the GntR-HutC family member YvoA from Bacillus subtilis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.1 M HEPES, PH 6.5, 1.26 M AMMONIUM SULPHATE, 0.111 M NDSB 256, 0.010 M NA-EDTA AND 1%(W/V) PEG 1000
Crystal Properties Matthews coefficient Solvent content 3 59.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 208.41 α = 90 b = 137.08 β = 94.97 c = 120.19 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 MARRESEARCH MIRRORS 2008-05-28 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 BESSY 14.2
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 2.4 45 96.4 0.13 9.2 1.4 249821 1.9 63.4
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 2.4 2.5 96.6 0.61 1.9
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 MAD THROUGHOUT NONE 2.4 114 117314 13035 99.3 0.205 0.199 0.2582 0.255 0.2613 RANDOM 64.5
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] 1.11 -0.25 -0.75 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.716 r_dihedral_angle_3_deg 18.144 r_dihedral_angle_4_deg 17.468 r_dihedral_angle_1_deg 5.861 r_scangle_it 1.967 r_angle_refined_deg 1.251 r_scbond_it 1.228 r_mcangle_it 0.619 r_mcbond_it 0.361 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.716 r_dihedral_angle_3_deg 18.144 r_dihedral_angle_4_deg 17.468 r_dihedral_angle_1_deg 5.861 r_scangle_it 1.967 r_angle_refined_deg 1.251 r_scbond_it 1.228 r_mcangle_it 0.619 r_mcbond_it 0.361 r_nbtor_refined 0.295 r_symmetry_vdw_refined 0.208 r_nbd_refined 0.196 r_symmetry_hbond_refined 0.163 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17771 Nucleic Acid Atoms Solvent Atoms 769 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling autoSHARP phasing