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Structure of KIAA1718, human Jumonji demethylase, in complex with N-oxalylglycine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YU2 PDB ENTRIES 2YU2 AND 1WEP experimental model PDB 1WEP PDB ENTRIES 2YU2 AND 1WEP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 5-10% (v/v) polyethylene glycol 3350, 0.2 M KSCN, and 0.1 M BisTris pH 6.0, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 3.67 66.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.7 α = 90 b = 125.6 β = 90 c = 206.1 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 CCD 2009-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID APS 22-ID
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 2.39 34.82 94.8 0.055 9.7 8 62010 21.1
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) 2.39 2.48 81.3 0.637 1.7 4.2
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRIES 2YU2 AND 1WEP 2.39 34.82 57397 2897 87.7 0.216 0.216 0.2145 0.245 RANDOM 41.6
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] -2.1 -11.38 13.48
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.3 c_scangle_it 2.26 c_mcangle_it 1.73 c_scbond_it 1.39 c_angle_deg 1.3 c_mcbond_it 0.97 c_improper_angle_d 0.78 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.3 c_scangle_it 2.26 c_mcangle_it 1.73 c_scbond_it 1.39 c_angle_deg 1.3 c_mcbond_it 0.97 c_improper_angle_d 0.78 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7101 Nucleic Acid Atoms Solvent Atoms 328 Heterogen Atoms 27
Software Software Software Name Purpose HKL-3000 data collection PHASER phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling