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Crystal structure of IdmH 96-104 loop truncation variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HNL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 3.6-4 M sodium formate, 10-15% (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 2.44 49.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.686 α = 90 b = 152.686 β = 90 c = 152.686 γ = 90
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 PILATUS3 6M 2017-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2 76.34 99.9 0.046 0.053 0.026 0.999 12.7 4.1 19992
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 99.9 0.516 1.4 4.1
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 6HNL 2 76.34 19006 974 99.82 0.22318 0.22107 0.2304 0.26754 0.2744 RANDOM 55.115
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.418 r_dihedral_angle_4_deg 18.977 r_dihedral_angle_3_deg 11.232 r_long_range_B_refined 6.398 r_long_range_B_other 6.397 r_dihedral_angle_1_deg 5.433 r_scangle_other 4.317 r_mcangle_it 4.15 r_mcangle_other 4.149 r_scbond_it 2.863
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.418 r_dihedral_angle_4_deg 18.977 r_dihedral_angle_3_deg 11.232 r_long_range_B_refined 6.398 r_long_range_B_other 6.397 r_dihedral_angle_1_deg 5.433 r_scangle_other 4.317 r_mcangle_it 4.15 r_mcangle_other 4.149 r_scbond_it 2.863 r_scbond_other 2.862 r_mcbond_other 2.739 r_mcbond_it 2.738 r_angle_refined_deg 1.261 r_angle_other_deg 0.884 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1935 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement TRUNCATE data reduction Aimless data scaling