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Crystal structure of the Apoform 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 2GD1 PDB ENTRY 2GD1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 10 % (W/V) PEG 8000, 100 MM NA/K PHOSPHATE BUFFER PH 6.2, 200 MM NACL
Crystal Properties Matthews coefficient Solvent content 2.18 43.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.3 α = 90 b = 110.7 β = 90 c = 138 γ = 90
Symmetry Space Group P 21 21 21
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 ESRF BEAMLINE BM30A ESRF BM30A
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 2.3 34.5 99.6 0.06 24.4 5.6 59159 -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 2.3 2.42 99.8 0.43 5.6 5.5
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 2GD1 2.3 34.5 56201 2958 100 0.20921 0.20621 0.2007 0.26636 0.2561 RANDOM 33.711
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] 0.7 -0.8 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.433 r_dihedral_angle_4_deg 20.718 r_dihedral_angle_3_deg 17.558 r_dihedral_angle_1_deg 6.73 r_scangle_it 3.389 r_scbond_it 2.082 r_mcangle_it 1.519 r_angle_refined_deg 1.468 r_mcbond_it 0.804 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.433 r_dihedral_angle_4_deg 20.718 r_dihedral_angle_3_deg 17.558 r_dihedral_angle_1_deg 6.73 r_scangle_it 3.389 r_scbond_it 2.082 r_mcangle_it 1.519 r_angle_refined_deg 1.468 r_mcbond_it 0.804 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 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 10086 Nucleic Acid Atoms Solvent Atoms 539 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing