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Apo-form of NAD-dependent formate dehydrogenase from higher-plant Arabidopsis thaliana
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Protein solution (2ul): 6 mg/ml FDH, 0.1M Na2HPO4, pH 7.0, 10 mM EDTA. Reservoir solution (2ul): 0.1M Bis-Tris, pH 6.0, 2.1M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.51 51.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.33 α = 90 b = 106.23 β = 90 c = 106.5 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 MAR CCD 165 mm M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.81 EMBL/DESY, HAMBURG X13
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 1.7 75.16 95.9 0.046 31.25 87821
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) 1.7 1.8 90.4 0.323 5.36
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.7 75.16 83414 83414 4407 99.43 0.16894 0.16747 0.174 0.19718 0.2016 RANDOM 28.692
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] -3.05 1.9 1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.784 r_dihedral_angle_4_deg 20.182 r_dihedral_angle_3_deg 13.925 r_dihedral_angle_1_deg 6.314 r_scangle_it 3.731 r_scbond_it 2.418 r_angle_refined_deg 1.589 r_mcangle_it 1.47 r_angle_other_deg 0.977 r_mcbond_it 0.886
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.784 r_dihedral_angle_4_deg 20.182 r_dihedral_angle_3_deg 13.925 r_dihedral_angle_1_deg 6.314 r_scangle_it 3.731 r_scbond_it 2.418 r_angle_refined_deg 1.589 r_mcangle_it 1.47 r_angle_other_deg 0.977 r_mcbond_it 0.886 r_mcbond_other 0.304 r_chiral_restr 0.1 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5417 Nucleic Acid Atoms Solvent Atoms 559 Heterogen Atoms 30
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction DNA data collection XDS data reduction