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Crystal structure of RpiR transcription factor from Sphaerobacter thermophilus (sugar isomerase domain)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 289 0.2 M sodium malonate, 20% PEG3350, in situ proteolysis with chymotrypsin, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.34 47.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.194 α = 90 b = 77.816 β = 94.89 c = 71.157 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 ADSC QUANTUM 210r mirrors 2011-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97911 APS 19-BM
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 1.8 50 99.8 0.072 3.8 68746 68642 -3 25.98
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 1.8 1.83 99.3 0.655 2 3.6 3358
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 1.8 35.45 68604 68604 1198 99.8 0.1735 0.1735 0.1729 0.1739 0.2092 0.2123 thin resolution shells 34.96
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] -8.0909 -0.7281 0.3685 7.7224
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 3.47 t_other_torsion 2.6 t_angle_deg 1.17 t_bond_d 0.015 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 3.47 t_other_torsion 2.6 t_angle_deg 1.17 t_bond_d 0.015 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5443 Nucleic Acid Atoms Solvent Atoms 304 Heterogen Atoms
Software Software Software Name Purpose SBC-Collect data collection SHELX model building MLPHARE phasing DM model building ARP/wARP model building Coot model building BUSTER refinement HKL-3000 data reduction HKL-3000 data scaling SHELX phasing DM phasing