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Crystal structure of Ubiquitin fold modifier 1 (Ufm1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IAA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 0.2M Ammonium acetate, 0.1M Sodium citrate tribasic dihydrate and 30% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.32 46.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.282 α = 90 b = 56.73 β = 90 c = 64.45 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray PIXEL DECTRIS PILATUS 6M-F M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 1.00800 ESRF ID30B
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 64.45 99.3 0.142 7.1 5.4 11636
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 2.11
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 5IAA 2 42.58 10994 607 98.94 0.19968 0.1981 0.2093 0.22961 0.2324 RANDOM 23.836
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] -0.91 1.4 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.364 r_dihedral_angle_4_deg 14.067 r_dihedral_angle_3_deg 12.4 r_dihedral_angle_1_deg 6.124 r_long_range_B_refined 4.072 r_long_range_B_other 3.877 r_scangle_other 1.857 r_angle_refined_deg 1.749 r_angle_other_deg 1.37 r_mcangle_other 1.337
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.364 r_dihedral_angle_4_deg 14.067 r_dihedral_angle_3_deg 12.4 r_dihedral_angle_1_deg 6.124 r_long_range_B_refined 4.072 r_long_range_B_other 3.877 r_scangle_other 1.857 r_angle_refined_deg 1.749 r_angle_other_deg 1.37 r_mcangle_other 1.337 r_mcangle_it 1.335 r_scbond_it 1.147 r_scbond_other 1.146 r_mcbond_it 0.862 r_mcbond_other 0.835 r_chiral_restr 0.109 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.007 r_gen_planes_other 0.006 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 1160 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing