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Crystal structure of Glycerol Trinitrate Reductase XdpB from Agrobacterium sp. R89-1 (Apo form)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.02 281 50 mM tri-Lithium citrate, 32 % (w/v) PEG 3350, not buffered
Crystal Properties Matthews coefficient Solvent content 2.14 42.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.885 α = 90 b = 68.599 β = 90 c = 93.677 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 PIXEL DECTRIS PILATUS 6M 2014-08-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2
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 2.1 47.36 94 0.068 13 3.7 21254 20170 20
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 2.1 2.16 86.6 0.358 2.1 3.4
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 MOLECULAR REPLACEMENT THROUGHOUT 2.1 47.36 20126 94.01 0.20091 0.198 0.2113 0.262 0.2167 Random selection 37
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] -2.16 4.62 -2.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.922 r_dihedral_angle_4_deg 17.458 r_dihedral_angle_3_deg 15.685 r_dihedral_angle_1_deg 6.388 r_long_range_B_refined 5.605 r_long_range_B_other 5.508 r_scangle_other 3.578 r_mcangle_it 3.307 r_mcangle_other 3.306 r_scbond_it 2.178
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.922 r_dihedral_angle_4_deg 17.458 r_dihedral_angle_3_deg 15.685 r_dihedral_angle_1_deg 6.388 r_long_range_B_refined 5.605 r_long_range_B_other 5.508 r_scangle_other 3.578 r_mcangle_it 3.307 r_mcangle_other 3.306 r_scbond_it 2.178 r_scbond_other 2.176 r_mcbond_it 2.077 r_mcbond_other 2.077 r_angle_refined_deg 1.417 r_angle_other_deg 0.81 r_chiral_restr 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2632 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling BALBES phasing