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L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT 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 VAPOR DIFFUSION, HANGING DROP 4.5 293 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 53.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.302 α = 90 b = 106.302 β = 90 c = 56.439 γ = 90
Symmetry Space Group P 4 21 2
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 1.75 20 92.6 0.06 23.03 7 30749 11.35
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 1.75 1.83 44.6 0.1 11.35 5.2
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 1.75 19.9 28595 2153 92.7 0.149 0.147 0.1496 0.172 0.1729 RANDOM 13.02
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] -0.28 -0.28 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.401 r_dihedral_angle_3_deg 13.059 r_dihedral_angle_4_deg 11.959 r_dihedral_angle_1_deg 5.383 r_scangle_it 2.176 r_scbond_it 1.459 r_angle_refined_deg 1.253 r_mcangle_it 0.796 r_mcbond_it 0.489 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.401 r_dihedral_angle_3_deg 13.059 r_dihedral_angle_4_deg 11.959 r_dihedral_angle_1_deg 5.383 r_scangle_it 2.176 r_scbond_it 1.459 r_angle_refined_deg 1.253 r_mcangle_it 0.796 r_mcbond_it 0.489 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.247 r_nbd_refined 0.218 r_symmetry_hbond_refined 0.185 r_xyhbond_nbd_refined 0.129 r_chiral_restr 0.076 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_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 2105 Nucleic Acid Atoms Solvent Atoms 277 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling CNS phasing