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X-ray Crystal Structure of a NADP(H)-bound Double Bond Reductase from Nicotiana tabacum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3J3H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 293 100mM KH2PO4/citrate buffer pH 4.5 + 45% PEG 300, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.53 51.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.2 α = 90 b = 149.84 β = 115.53 c = 66.61 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS PILATUS 6M 2011-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.979 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.9 60.11 5.8 59835
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 3J3H 1.9 57.83 2 56799 3035 97.68 0.17456 0.17291 0.178 0.20553 0.2111 RANDOM 27.215
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] -0.04 -0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.646 r_dihedral_angle_4_deg 18.22 r_dihedral_angle_3_deg 14.761 r_dihedral_angle_1_deg 6.273 r_scangle_it 4.059 r_scbond_it 2.557 r_mcangle_it 1.64 r_angle_refined_deg 1.612 r_mcbond_it 0.92 r_chiral_restr 0.119
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.646 r_dihedral_angle_4_deg 18.22 r_dihedral_angle_3_deg 14.761 r_dihedral_angle_1_deg 6.273 r_scangle_it 4.059 r_scbond_it 2.557 r_mcangle_it 1.64 r_angle_refined_deg 1.612 r_mcbond_it 0.92 r_chiral_restr 0.119 r_bond_refined_d 0.016 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5027 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms 96
Software Software Software Name Purpose GDA data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling