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Structure of Escherichia coli ribose-5-phosphate isomerase, RpiA, complexed with arabinose-5-phosphate.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KS2 PDB ENTRY 1KS2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 CRYSTALS WERE GROWN FROM A SOLUTION CONTAINING 3.5 MG/ML PROTEIN, 30-35 % PEG 4000 10 MM ARABINOSE-5-PHOSPHATE, 0.05M TRIS-HCL PH 8.4, 0.1 M MGCL2
Crystal Properties Matthews coefficient Solvent content 2.3 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.049 α = 90.23 b = 42.4 β = 100.98 c = 60.195 γ = 98.98
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 CCD GE(220),HORIZONTAL FOCUSING MULTILAYER 2002-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.25 40 81.8 0.095 12.4 4.3 90067
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 1.25 1.32 40.1 0.76 1.1 3.6
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 PDB ENTRY 1KS2 1.25 40 86708 4498 81.8 0.224 0.224 0.2268 0.24 0.243 RANDOM 10.26
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] -0.54 -0.68 0.25 -0.48 -0.3 0.89
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 3.122 r_scbond_it 2.236 r_angle_other_deg 1.863 r_mcangle_it 1.147 r_mcbond_it 0.775 r_symmetry_hbond_refined 0.507 r_nbd_refined 0.22 r_symmetry_vdw_refined 0.161 r_xyhbond_nbd_refined 0.116 r_chiral_restr 0.108
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 3.122 r_scbond_it 2.236 r_angle_other_deg 1.863 r_mcangle_it 1.147 r_mcbond_it 0.775 r_symmetry_hbond_refined 0.507 r_nbd_refined 0.22 r_symmetry_vdw_refined 0.161 r_xyhbond_nbd_refined 0.116 r_chiral_restr 0.108 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d r_angle_refined_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2771 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing