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Structure of ribB complexed with substrate Ru5P
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4P6D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.1 293 Na2HPO4, PEG3350
Crystal Properties Matthews coefficient Solvent content 2.05 39.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.408 α = 90 b = 74.086 β = 90 c = 99.331 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 2010-06-25 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 99.4 0.085 19.2 6.9 26194 -3 24.43
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 97.8 0.535 3.7 6.6
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 4P6D 2.04 20 24866 1328 99.39 0.17589 0.17338 0.1823 0.22356 0.2235 RANDOM 29.592
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] 2.23 -1.05 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.451 r_dihedral_angle_3_deg 13.754 r_dihedral_angle_4_deg 13.463 r_dihedral_angle_1_deg 5.782 r_long_range_B_refined 5.155 r_long_range_B_other 5.155 r_scangle_other 3.07 r_mcangle_it 2.261 r_mcangle_other 2.261 r_scbond_it 1.898
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.451 r_dihedral_angle_3_deg 13.754 r_dihedral_angle_4_deg 13.463 r_dihedral_angle_1_deg 5.782 r_long_range_B_refined 5.155 r_long_range_B_other 5.155 r_scangle_other 3.07 r_mcangle_it 2.261 r_mcangle_other 2.261 r_scbond_it 1.898 r_scbond_other 1.896 r_mcbond_it 1.455 r_mcbond_other 1.454 r_angle_refined_deg 1.31 r_angle_other_deg 0.752 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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 3196 Nucleic Acid Atoms Solvent Atoms 284 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing