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Crystal structure of Domain Related to Iron (DRI) in complex with heme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other native model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 23% PEG3350, 100 mM Bis-Tris, pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.24 45.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.976 α = 90 b = 42.976 β = 90 c = 379.484 γ = 120
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 EIGER X 16M 2019-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.979 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 3 50 92.6 0.092 0.98 6 3.5 7898
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.08 0.504 0.969
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3 37.25 6550 763 92.6 0.20602 0.20122 0.2016 0.27914 0.2831 RANDOM 65.834
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] 2.58 1.29 2.58 -8.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.481 r_dihedral_angle_3_deg 22.697 r_dihedral_angle_4_deg 22.117 r_long_range_B_other 12.108 r_long_range_B_refined 12.106 r_mcangle_other 8.759 r_mcangle_it 8.758 r_scangle_other 8.228 r_dihedral_angle_1_deg 6.888 r_mcbond_other 5.569
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.481 r_dihedral_angle_3_deg 22.697 r_dihedral_angle_4_deg 22.117 r_long_range_B_other 12.108 r_long_range_B_refined 12.106 r_mcangle_other 8.759 r_mcangle_it 8.758 r_scangle_other 8.228 r_dihedral_angle_1_deg 6.888 r_mcbond_other 5.569 r_mcbond_it 5.566 r_scbond_it 5.37 r_scbond_other 5.368 r_angle_refined_deg 2.08 r_angle_other_deg 1.227 r_chiral_restr 0.058 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.005 r_gen_planes_other 0.003 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2724 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 90
Software Software Software Name Purpose ADSC data collection autoPROC data reduction autoPROC data scaling PHASER phasing REFMAC refinement