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Crystal Structure of Brugia malayi Deoxyhypusine synthase (DHPS)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RQD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20% PEG3350 0.2M ammonium citrate dibasic
Crystal Properties Matthews coefficient Solvent content 2.19 43.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.753 α = 90 b = 136.32 β = 92.92 c = 75.883 γ = 90
Symmetry Space Group P 1 21 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 Oxford Danfysik/SESO Two stage demagnification using two K-B pairs of bimorph type mirrors 2018-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96858 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.3 29.42 99.6 0.129 0.155 0.084 0.992 5.4 3.3 62547
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.36 99.7 0.88 1.048 0.563 0.565 3.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1RQD 2.3 29.41 59634 2885 99.55 0.1894 0.1882 0.2157 0.2069 RANDOM 34.024
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] 0.62 1.55 -2.53 1.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.78 r_dihedral_angle_4_deg 16.259 r_dihedral_angle_3_deg 13.151 r_dihedral_angle_1_deg 6.08 r_angle_refined_deg 1.259 r_angle_other_deg 1.233 r_chiral_restr 0.055 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.78 r_dihedral_angle_4_deg 16.259 r_dihedral_angle_3_deg 13.151 r_dihedral_angle_1_deg 6.08 r_angle_refined_deg 1.259 r_angle_other_deg 1.233 r_chiral_restr 0.055 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10533 Nucleic Acid Atoms Solvent Atoms 397 Heterogen Atoms 163
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction