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Factor Inhibiting HIF D201E in Complex with Fe, and Alpha-Ketoglutarate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D8C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1M Hepes, 1.6mM ammonium sulfate, 3% PEG 400
Crystal Properties Matthews coefficient Solvent content 3.41 63.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.131 α = 90 b = 86.131 β = 90 c = 149.213 γ = 90
Symmetry Space Group P 41 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 ADSC QUANTUM 270 FOCUSING MIRRORS 2013-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 1.08 NSLS X6A
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 2.3 50 99.4 0.124 10.4 8 25594
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 2.3 2.34 100 0.884 7.9
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 3D8C 2.3 29.84 20805 1773 87.8 0.19 0.187 0.1955 0.227 0.2324 RANDOM 66.26
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] -0.95 -0.95 1.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.123 r_dihedral_angle_4_deg 20.833 r_dihedral_angle_3_deg 17.442 r_dihedral_angle_1_deg 7.003 r_mcangle_it 6.192 r_mcbond_it 4.126 r_mcbond_other 4.123 r_angle_refined_deg 1.767 r_angle_other_deg 0.903 r_chiral_restr 0.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.123 r_dihedral_angle_4_deg 20.833 r_dihedral_angle_3_deg 17.442 r_dihedral_angle_1_deg 7.003 r_mcangle_it 6.192 r_mcbond_it 4.126 r_mcbond_other 4.123 r_angle_refined_deg 1.767 r_angle_other_deg 0.903 r_chiral_restr 0.105 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2770 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing