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Crystal structure of IUnH from Leishmania braziliensis in complex with D-Ribose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EZR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 0.2M Ammonium acetate, 0.1M HEPES pH 7.5 and 45% MPD
Crystal Properties Matthews coefficient Solvent content 3.16 61.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.66 α = 90 b = 94.08 β = 90 c = 123.12 γ = 90
Symmetry Space Group I 2 2 2
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 2M 2015-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.459 LNLS W01B-MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.53 74.754 98.5 0.091 6.9 4.3 64501
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 1.53 1.61 90.8 0.431 0.7 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1EZR 1.53 21.655 1.33 64118 3226 97.82 0.1542 0.1534 0.1685 0.2102 24.5624
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 f_dihedral_angle_d 4.71 f_angle_d 0.972 f_chiral_restr 0.062 f_bond_d 0.011 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2398 Nucleic Acid Atoms Solvent Atoms 278 Heterogen Atoms 11
Software Software Software Name Purpose SCALA data scaling MOLREP phasing PHENIX refinement PDB_EXTRACT data extraction MOSFLM data reduction MOLREP phasing