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Crystal structure of Ofd2 in complex with 2OG from Schizosaccharomyces pombe
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3THP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 18% MPEG 5000, 0.1M HEPES, pH 7.4
Crystal Properties Matthews coefficient Solvent content 2.78 55.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.114 α = 90 b = 80.312 β = 90 c = 82.607 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 293 CCD ADSC QUANTUM 315 2014-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.9791 SSRF BL17U1
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 57.58 99.9 0.06 2.4 8.3 15373
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3THP 2 57.58 15373 813 99.23 0.2026 0.2002 0.213 0.2465 0.2508 RANDOM 42.105
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] 3.85 -3.47 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.005 r_dihedral_angle_4_deg 19.159 r_dihedral_angle_3_deg 16.259 r_dihedral_angle_1_deg 7.289 r_angle_refined_deg 1.091 r_angle_other_deg 0.6 r_chiral_restr 0.075 r_gen_planes_refined 0.012 r_bond_refined_d 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.005 r_dihedral_angle_4_deg 19.159 r_dihedral_angle_3_deg 16.259 r_dihedral_angle_1_deg 7.289 r_angle_refined_deg 1.091 r_angle_other_deg 0.6 r_chiral_restr 0.075 r_gen_planes_refined 0.012 r_bond_refined_d 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1495 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 15
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction MOLREP phasing