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Structure of an active site mutant of the D-Erythrose-4-Phosphate Dehydrogenase from E. coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X5J PDB ENTRY 2X5J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 24 % (W/V) PEG 1000, 100 MM TRIS-HCL BUFFER PH 8.5, 3 MM ERYTHROSE-4-PHOSPHATE
Crystal Properties Matthews coefficient Solvent content 3.45 64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.81 α = 90 b = 134.81 β = 90 c = 246.11 γ = 90
Symmetry Space Group P 41 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 ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
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 2.37 56 98.6 0.08 28.1 10.2 91660 -3
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 2.37 2.5 93.1 0.77 4.5 5.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2X5J 2.37 55.97 87182 4579 98.78 0.16656 0.16444 0.20699 0.2018 RANDOM 32.92
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] -0.04 -0.04 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.097 r_dihedral_angle_4_deg 20.144 r_dihedral_angle_3_deg 16.093 r_dihedral_angle_1_deg 6.823 r_scangle_it 5.717 r_scbond_it 3.609 r_mcangle_it 2.172 r_angle_refined_deg 1.963 r_mcbond_it 1.165 r_chiral_restr 0.133
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.097 r_dihedral_angle_4_deg 20.144 r_dihedral_angle_3_deg 16.093 r_dihedral_angle_1_deg 6.823 r_scangle_it 5.717 r_scbond_it 3.609 r_mcangle_it 2.172 r_angle_refined_deg 1.963 r_mcbond_it 1.165 r_chiral_restr 0.133 r_bond_refined_d 0.023 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_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 10354 Nucleic Acid Atoms Solvent Atoms 956 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing