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Structure of the C-terminally extended domain My4 of human myomesin (space group P65)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FM5 PDB ENTRY 5FM5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.8 21 % (W/V) PEG 2000 MME, 10 MM NICL2, 100 MM TRIS/HCL PH 8.8
Crystal Properties Matthews coefficient Solvent content 3.01 59.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.41 α = 90 b = 97.41 β = 90 c = 106.15 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 PILATUS 6M 2015-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 2.05 84.36 99.9 0.13 13.4 20 35371 -1
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 2.05 2.11 98.7 1.5 1.6 20
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 PDB ENTRY 5FM5 2.05 84.36 33912 1774 99.91 0.19364 0.19242 0.1925 0.21687 0.2163 RANDOM 50.102
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] 22.92 22.92 -45.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.841 r_dihedral_angle_4_deg 19.223 r_dihedral_angle_3_deg 15.772 r_dihedral_angle_1_deg 7.098 r_angle_refined_deg 1.716 r_mcangle_it 1.689 r_angle_other_deg 1.457 r_mcbond_it 1.074 r_mcbond_other 1.069 r_scbond_it 0.982
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.841 r_dihedral_angle_4_deg 19.223 r_dihedral_angle_3_deg 15.772 r_dihedral_angle_1_deg 7.098 r_angle_refined_deg 1.716 r_mcangle_it 1.689 r_angle_other_deg 1.457 r_mcbond_it 1.074 r_mcbond_other 1.069 r_scbond_it 0.982 r_chiral_restr 0.096 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.008 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_mcangle_other 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 3084 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 10
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing MOLREP phasing REFMAC refinement