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Thermotoga maritima Ribose Binding Protein Unliganded Form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DRI PDB ENTRY 2DRI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 5.9 290 0.2M NaCl, 0.1M Bis-Tris pH5.9, 25% PEG 3350, MICRO-BATCH, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.32 46.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.901 α = 90 b = 136.826 β = 90 c = 144.465 γ = 90
Symmetry Space Group F 2 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 MARMOSAIC 300 mm CCD 2005-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.997 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.4 50 99 0.05 5.8 115461 115461
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.45 91.4 91.4 0.515 1.7 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2DRI 1.4 50 115460 115460 5767 98.97 0.181 0.181 0.18 0.1802 0.203 0.203 RANDOM 14.532
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] -0.42 0.38 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.25 r_dihedral_angle_4_deg 17.466 r_dihedral_angle_3_deg 12.6 r_dihedral_angle_1_deg 5.223 r_scangle_it 2.914 r_scbond_it 2.144 r_angle_refined_deg 1.199 r_mcangle_it 1.119 r_mcbond_it 1.052 r_angle_other_deg 0.755
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.25 r_dihedral_angle_4_deg 17.466 r_dihedral_angle_3_deg 12.6 r_dihedral_angle_1_deg 5.223 r_scangle_it 2.914 r_scbond_it 2.144 r_angle_refined_deg 1.199 r_mcangle_it 1.119 r_mcbond_it 1.052 r_angle_other_deg 0.755 r_symmetry_vdw_other 0.237 r_nbd_refined 0.208 r_nbtor_refined 0.184 r_nbd_other 0.174 r_mcbond_other 0.173 r_symmetry_vdw_refined 0.138 r_symmetry_hbond_refined 0.135 r_xyhbond_nbd_refined 0.131 r_nbtor_other 0.082 r_chiral_restr 0.073 r_xyhbond_nbd_other 0.047 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4362 Nucleic Acid Atoms Solvent Atoms 627 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction AMoRE phasing