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Crystal structure of Ribokinase (TM0960) from Thermotoga maritima at 2.15 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GQT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 293 0.4M (NH4)2Tartrate, 0.4% PEG-3350, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.34 47.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.142 α = 90 b = 45.265 β = 93.3 c = 77.26 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 ADSC 2004-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 ALS 5.0.3
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 60.4 92.3 0.07 10 3.2 39375 37.9
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 2.05 61.2 0.682 1.3 1.9 1884
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 MOLECULAR REPLACEMENT THROUGHOUT 1gqt 2.15 60.4 32122 1676 97.96 0.19189 0.18954 0.1981 0.23539 0.24 RANDOM 31.282
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] 1.99 0.85 -1.2 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.216 r_dihedral_angle_4_deg 21.355 r_dihedral_angle_3_deg 14.158 r_dihedral_angle_1_deg 6.023 r_scangle_it 2.376 r_scbond_it 1.559 r_angle_refined_deg 1.477 r_angle_other_deg 0.862 r_mcangle_it 0.839 r_mcbond_it 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.216 r_dihedral_angle_4_deg 21.355 r_dihedral_angle_3_deg 14.158 r_dihedral_angle_1_deg 6.023 r_scangle_it 2.376 r_scbond_it 1.559 r_angle_refined_deg 1.477 r_angle_other_deg 0.862 r_mcangle_it 0.839 r_mcbond_it 0.55 r_symmetry_hbond_refined 0.254 r_nbd_refined 0.202 r_symmetry_vdw_other 0.186 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.178 r_nbd_other 0.177 r_symmetry_vdw_refined 0.16 r_mcbond_other 0.16 r_nbtor_other 0.087 r_chiral_restr 0.081 r_xyhbond_nbd_other 0.059 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4537 Nucleic Acid Atoms Solvent Atoms 279 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement CCP4 data scaling