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Structural Genomics, the crystal structure of a putative transcriptional regulator GntR from Rhodococcus sp. RHA1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 298 35% Tacsimate, 0.1M Sodium Acetate, 2% PEG5000 MME, 2mM Cysteine, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.97 58.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.052 α = 90 b = 108.052 β = 90 c = 107.26 γ = 90
Symmetry Space Group I 4 2 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 mirror 2006-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97932 APS 19-ID
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 2.2 38.21 97.9 0.076 31.84 7.4 16123 16123
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 2.25 81.1 0.54 2.44 4.9 869
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2.2 38.21 15289 15289 815 97.86 0.19673 0.19673 0.1941 0.1952 0.24851 0.2426 RANDOM 43.5
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] -0.01 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.303 r_dihedral_angle_4_deg 22.403 r_dihedral_angle_3_deg 19.604 r_scangle_it 7.243 r_dihedral_angle_1_deg 6.737 r_scbond_it 4.701 r_mcangle_it 2.965 r_angle_refined_deg 2.599 r_mcbond_it 2.148 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.303 r_dihedral_angle_4_deg 22.403 r_dihedral_angle_3_deg 19.604 r_scangle_it 7.243 r_dihedral_angle_1_deg 6.737 r_scbond_it 4.701 r_mcangle_it 2.965 r_angle_refined_deg 2.599 r_mcbond_it 2.148 r_nbtor_refined 0.312 r_symmetry_hbond_refined 0.284 r_chiral_restr 0.229 r_nbd_refined 0.224 r_symmetry_vdw_refined 0.223 r_xyhbond_nbd_refined 0.18 r_bond_refined_d 0.037 r_gen_planes_refined 0.014 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1618 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling HKL-3000 phasing SHELXE model building SOLVE phasing RESOLVE phasing ARP/wARP model building