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D-Erythronate-4-Phosphate Dehydrogenase complexed with NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O4C PDBID 2O4C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 25% PEG 3350,0.2M NH4 Acetate, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.42 49.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.279 α = 90 b = 167.765 β = 93.88 c = 103.949 γ = 90
Symmetry Space Group P 1 21 1
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 MARMOSAIC 300 mm CCD MIRRORS 2010-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97950 APS 21-ID-D
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 2.36 103.7 99.5 0.08 20.3 6.6 128763 128763 -3 51.9
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) 2.36 2.39 99.9 0.64 2.9 6.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDBID 2O4C 2.36 30.19 122293 122293 6470 98.58 0.19346 0.1903 0.1895 0.25331 0.2533 RANDOM 46.667
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] -1.05 1.24 0.13 1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.606 r_dihedral_angle_4_deg 21.222 r_dihedral_angle_3_deg 16.496 r_dihedral_angle_1_deg 5.802 r_scangle_it 3.747 r_scbond_it 2.401 r_angle_refined_deg 1.46 r_mcangle_it 1.183 r_mcbond_it 0.602 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.606 r_dihedral_angle_4_deg 21.222 r_dihedral_angle_3_deg 16.496 r_dihedral_angle_1_deg 5.802 r_scangle_it 3.747 r_scbond_it 2.401 r_angle_refined_deg 1.46 r_mcangle_it 1.183 r_mcbond_it 0.602 r_chiral_restr 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22878 Nucleic Acid Atoms Solvent Atoms 556 Heterogen Atoms 352
Software Software Software Name Purpose Blu-Ice data collection CCP4 model building MrBUMP phasing PHENIX model building REFMAC refinement HKL-2000 data reduction HKL-3000 data scaling CCP4 phasing PHENIX phasing