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CRYSTAL STRUCTURE OF E. COLI K-12 YHDH WITH BOUND NADPH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O89 NATIVE YHD, PDB ID CODE 1O89
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 8.5 % PEG 8K, 0.1 M NA-ACETATE PH 5.5, 0.01 MM ZNCL2, 5 MM NADPH
Crystal Properties Matthews coefficient Solvent content 3.4 63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 189.313 α = 90 b = 189.313 β = 90 c = 98.654 γ = 120
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 2002-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 2.6 43.7 100 0.05 8.3 6.1 62012
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 2.6 2.67 100 0.192 3.9 5.9
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 NATIVE YHD, PDB ID CODE 1O89 2.6 158.11 58842 3140 100 0.173 0.171 0.1935 0.202 0.2169 RANDOM
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] 0.2 0.1 0.2 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.897 r_angle_refined_deg 1.226 r_angle_other_deg 0.776 r_symmetry_vdw_other 0.254 r_nbd_other 0.231 r_nbd_refined 0.19 r_symmetry_vdw_refined 0.172 r_xyhbond_nbd_refined 0.168 r_symmetry_hbond_refined 0.156 r_nbtor_other 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.897 r_angle_refined_deg 1.226 r_angle_other_deg 0.776 r_symmetry_vdw_other 0.254 r_nbd_other 0.231 r_nbd_refined 0.19 r_symmetry_vdw_refined 0.172 r_xyhbond_nbd_refined 0.168 r_symmetry_hbond_refined 0.156 r_nbtor_other 0.082 r_chiral_restr 0.067 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 9752 Nucleic Acid Atoms Solvent Atoms 348 Heterogen Atoms 192
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALA data scaling MOLREP phasing