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Structure of ribB complexed with substrate (Ru5P) and metal ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G58
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.1 293 PEG3350, Na2HPO4
Crystal Properties Matthews coefficient Solvent content 2.08 40.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.079 α = 90 b = 77.09 β = 90 c = 97.531 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate Mirror 2010-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.04 20 98.3 0.065 23.1 7.3 25330 -3 21
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 2.04 2.16 92.7 0.258 6.4 6.1
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 1G58 2.04 20 24042 1287 98.5 0.17844 0.1756 0.184 0.23216 0.2349 RANDOM 22.487
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] -1.13 1.97 -0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.823 r_dihedral_angle_4_deg 14.013 r_dihedral_angle_3_deg 13.17 r_dihedral_angle_1_deg 5.288 r_long_range_B_refined 3.575 r_long_range_B_other 3.574 r_scangle_other 1.742 r_mcangle_it 1.366 r_mcangle_other 1.366 r_angle_refined_deg 1.147
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.823 r_dihedral_angle_4_deg 14.013 r_dihedral_angle_3_deg 13.17 r_dihedral_angle_1_deg 5.288 r_long_range_B_refined 3.575 r_long_range_B_other 3.574 r_scangle_other 1.742 r_mcangle_it 1.366 r_mcangle_other 1.366 r_angle_refined_deg 1.147 r_scbond_it 1.047 r_scbond_other 1.047 r_mcbond_it 0.831 r_mcbond_other 0.826 r_angle_other_deg 0.721 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3265 Nucleic Acid Atoms Solvent Atoms 277 Heterogen Atoms 70
Software Software Software Name Purpose XDS data scaling REFMAC refinement PHASER phasing