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L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT E117S- E192A-K248G-R253A-E254A)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OJR PDB ENTRY 1OJR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.5 40% (V/V) 1,2-PROPANEDIOL, 50 MM CA ACETATE, 100 MM ACETATE BUFFER (PH 4.5)
Crystal Properties Matthews coefficient Solvent content 2.7 54.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.23 α = 90 b = 84.23 β = 90 c = 91.747 γ = 90
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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 1.5 50 87.9 0.04 17.05 3.93 44912 2.72
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 1.5 1.56 78.5 0.32 2.72 2.51
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 1OJR 1.5 36.35 42664 2246 87.9 0.167 0.166 0.1675 0.184 0.1829 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.427 r_dihedral_angle_3_deg 13.254 r_dihedral_angle_4_deg 6.964 r_dihedral_angle_1_deg 5.46 r_scangle_it 2.716 r_scbond_it 1.813 r_angle_refined_deg 1.395 r_mcangle_it 1.076 r_mcbond_it 0.666 r_metal_ion_refined 0.349
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.427 r_dihedral_angle_3_deg 13.254 r_dihedral_angle_4_deg 6.964 r_dihedral_angle_1_deg 5.46 r_scangle_it 2.716 r_scbond_it 1.813 r_angle_refined_deg 1.395 r_mcangle_it 1.076 r_mcbond_it 0.666 r_metal_ion_refined 0.349 r_nbtor_refined 0.307 r_symmetry_hbond_refined 0.234 r_nbd_refined 0.217 r_symmetry_vdw_refined 0.199 r_xyhbond_nbd_refined 0.157 r_chiral_restr 0.09 r_symmetry_metal_ion_refined 0.064 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other 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 2085 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling CNS phasing