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The crystal structure of JMJD2A complexed with Ni and N-oxalylglycine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GP3 PDB entry 2gp3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277 20% PEG 3350, 0.1M citrate, 2 mM NiCl2, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.43 49.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.12 α = 90 b = 148.531 β = 90 c = 57.333 γ = 90
Symmetry Space Group P 21 21 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 CCD MARMOSAIC 225 mm CCD 2006-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.99900 SLS X10SA
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 2.15 59.87 94.5 0.078 10.4 3.2 45023 45023 36
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 2.15 2.27 96.5 0.485 2.1 3.2 6601
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 FOURIER SYNTHESIS THROUGHOUT PDB entry 2gp3 2.15 50 43072 43072 1912 94.06 0.17876 0.17876 0.17654 0.1816 0.228 0.2322 RANDOM 29.938
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] -0.35 -0.8 1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.465 r_dihedral_angle_4_deg 17.523 r_dihedral_angle_3_deg 15.496 r_scangle_it 7.292 r_dihedral_angle_1_deg 6.832 r_scbond_it 6.068 r_mcangle_it 3.972 r_mcbond_it 2.9 r_angle_refined_deg 1.583 r_angle_other_deg 0.981
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.465 r_dihedral_angle_4_deg 17.523 r_dihedral_angle_3_deg 15.496 r_scangle_it 7.292 r_dihedral_angle_1_deg 6.832 r_scbond_it 6.068 r_mcangle_it 3.972 r_mcbond_it 2.9 r_angle_refined_deg 1.583 r_angle_other_deg 0.981 r_mcbond_other 0.841 r_symmetry_hbond_refined 0.231 r_symmetry_vdw_other 0.209 r_nbd_refined 0.199 r_nbd_other 0.191 r_nbtor_refined 0.186 r_symmetry_vdw_refined 0.147 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.095 r_nbtor_other 0.091 r_metal_ion_refined 0.064 r_bond_refined_d 0.017 r_xyhbond_nbd_other 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5536 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction CCP4 data scaling