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Crystal Structure of D-Erythronate-4-phosphate Dehydrogenase Complexed with NAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 297 0.7M ammonium dihydrogen phosphate, 0.4M ammonium tartrate, 0.1M sodium citrate (pH 5.6), 10mM cupric chloride, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 3.76 67.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.914 α = 90 b = 101.63 β = 90 c = 142.994 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 ADSC QUANTUM 210 mirrors 2004-06-25 M MAD 2 1 x-ray 100 CCD ADSC QUANTUM 210 mirrors 2004-06-25 M SINGLE WAVELENGTH 3 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 0.97930, 0.97946, 0.95000 Photon Factory AR-NW12A 2 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.00000 Photon Factory AR-NW12A
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 2.2 30 99.9 0.049 14.6 63477
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 2.2 2.28 100 0.442 6245
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.3 19.77 55468 5563 99.83 0.229 0.225 0.2218 0.259 0.256 RANDOM 44.484
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.975 r_dihedral_angle_4_deg 18.437 r_dihedral_angle_3_deg 15.72 r_dihedral_angle_1_deg 5.229 r_scangle_it 2.073 r_scbond_it 1.283 r_angle_refined_deg 1.173 r_mcangle_it 0.99 r_mcbond_it 0.589 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.975 r_dihedral_angle_4_deg 18.437 r_dihedral_angle_3_deg 15.72 r_dihedral_angle_1_deg 5.229 r_scangle_it 2.073 r_scbond_it 1.283 r_angle_refined_deg 1.173 r_mcangle_it 0.99 r_mcbond_it 0.589 r_nbtor_refined 0.297 r_nbd_refined 0.19 r_symmetry_vdw_refined 0.17 r_xyhbond_nbd_refined 0.137 r_symmetry_hbond_refined 0.112 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5772 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 109
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction