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Thermotoga maritima Ribose Binding Protein Ribose Bound 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 6 290 0.1M RbCl, 0.1M MES pH6.0, 20% PEG 8,000, Micro-Batch, temperature 290K
Crystal Properties Matthews coefficient Solvent content 3.43 64.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.07 α = 90 b = 98.242 β = 90 c = 131.099 γ = 90
Symmetry Space Group I 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 2005-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.97944 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 2 50 80.9 0.056 25.7 5.8 25783 25783
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 2 2.07 21 0.284 3.6 1.6 653
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 2.15 50 23715 23715 1179 92.17 0.194 0.194 0.193 0.2001 0.223 0.2306 RANDOM 32.1
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] -0.35 -0.78 1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.897 r_dihedral_angle_4_deg 16.433 r_dihedral_angle_3_deg 15.227 r_dihedral_angle_1_deg 6.781 r_scangle_it 2.311 r_scbond_it 1.616 r_angle_refined_deg 1.246 r_mcangle_it 1.095 r_mcbond_it 0.977 r_angle_other_deg 0.812
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.897 r_dihedral_angle_4_deg 16.433 r_dihedral_angle_3_deg 15.227 r_dihedral_angle_1_deg 6.781 r_scangle_it 2.311 r_scbond_it 1.616 r_angle_refined_deg 1.246 r_mcangle_it 1.095 r_mcbond_it 0.977 r_angle_other_deg 0.812 r_symmetry_vdw_other 0.221 r_nbd_refined 0.196 r_nbtor_refined 0.179 r_nbd_other 0.178 r_xyhbond_nbd_refined 0.136 r_mcbond_other 0.123 r_symmetry_vdw_refined 0.103 r_symmetry_hbond_refined 0.092 r_nbtor_other 0.086 r_chiral_restr 0.076 r_bond_refined_d 0.012 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 2286 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 10
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection AMoRE phasing