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Crystal structure of human HO1 H25R
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N45
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 100 mM HEPES, pH 7.4; 2.1 M (NH4)2SO4; 0.9% 1,6-hexane-diol; BIG_CHAP
Crystal Properties Matthews coefficient Solvent content 1.83 32.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.08 α = 90 b = 54.41 β = 99.09 c = 122.28 γ = 90
Symmetry Space Group P 1 21 1
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 315 2014-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.95 74.1 97.4 8.7 6.6 20111
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.95 3.11 92.4 2 6.3
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 1N45 2.95 70.1 19055 1052 97.3 0.20608 0.20326 0.2082 0.25859 0.267 RANDOM 50.051
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] -0.94 -1.16 -2.74 3.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.12 r_dihedral_angle_4_deg 15.812 r_dihedral_angle_3_deg 15.634 r_long_range_B_refined 7.5 r_long_range_B_other 7.5 r_scangle_other 4.932 r_dihedral_angle_1_deg 4.688 r_mcangle_it 4.266 r_mcangle_other 4.266 r_scbond_it 2.851
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.12 r_dihedral_angle_4_deg 15.812 r_dihedral_angle_3_deg 15.634 r_long_range_B_refined 7.5 r_long_range_B_other 7.5 r_scangle_other 4.932 r_dihedral_angle_1_deg 4.688 r_mcangle_it 4.266 r_mcangle_other 4.266 r_scbond_it 2.851 r_scbond_other 2.851 r_mcbond_it 2.556 r_mcbond_other 2.551 r_angle_refined_deg 1.388 r_angle_other_deg 1.075 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.004 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 6984 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 202
Software Software Software Name Purpose REFMAC refinement