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L-rhamnulose-1-phosphate aldolase from Escherichia coli (mutant E192A)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GT7 PDB ENTRY 1GT7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 HANGING DROP WITH 5 MG/ML PROTEIN AND 18% (V/V) DIOXANE. RESERVOIR WITH 35% (V/V) DIOXANE. HAMPTON CRYSTAL SCREEN-2 NO.4, pH 4.00
Crystal Properties Matthews coefficient Solvent content 2.8 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.024 α = 90 b = 108.024 β = 90 c = 57.166 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 IMAGE PLATE MARRESEARCH 1999-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B EMBL/DESY, HAMBURG BW7B
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 1.35 30.5 96 0.052 8.7 3.7 71387 10.6
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 1.35 1.4 95 0.38 1.7 3.4
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 1GT7 1.35 30.43 69212 2175 95.8 0.112 0.111 0.1284 0.142 0.1536 RANDOM 12.43
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] -0.27 -0.27 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.776 r_scangle_it 5.99 r_scbond_it 4.896 r_dihedral_angle_1_deg 4.067 r_mcangle_it 3.696 r_mcbond_it 2.842 r_angle_refined_deg 1.252 r_angle_other_deg 1.112 r_symmetry_hbond_refined 0.283 r_symmetry_vdw_refined 0.278
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.776 r_scangle_it 5.99 r_scbond_it 4.896 r_dihedral_angle_1_deg 4.067 r_mcangle_it 3.696 r_mcbond_it 2.842 r_angle_refined_deg 1.252 r_angle_other_deg 1.112 r_symmetry_hbond_refined 0.283 r_symmetry_vdw_refined 0.278 r_nbd_refined 0.229 r_nbtor_other 0.229 r_symmetry_vdw_other 0.196 r_xyhbond_nbd_refined 0.191 r_nbd_other 0.188 r_xyhbond_nbd_other 0.179 r_metal_ion_refined 0.101 r_chiral_restr 0.086 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_metal_ion_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 2120 Nucleic Acid Atoms Solvent Atoms 525 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing