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Crystal structure of the human myomesin domain 10
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Y23
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 291 0.1 M citrate/phosphate buffer pH 5.4, 30 % PEG3350
Crystal Properties Matthews coefficient Solvent content 2.09 41.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.599 α = 90 b = 58.599 β = 90 c = 62.821 γ = 90
Symmetry Space Group P 43 21 2
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 300K 2013-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918409 BESSY 14.1
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 1.8 42.85 99.7 0.025 0.031 0.017 1 2.5 5.2 55419 10591 30.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 99.9 0.572 0.706 0.408 0.829 2.5 5.4
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2Y23 1.8 42.85 10572 99.33 0.20471 0.1983 0.2124 0.244 38.438
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] -0.04 -0.04 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.968 r_dihedral_angle_4_deg 23.221 r_dihedral_angle_3_deg 18.216 r_dihedral_angle_1_deg 7.547 r_long_range_B_refined 6.399 r_long_range_B_other 6.322 r_scangle_other 3.334 r_mcangle_it 2.47 r_mcangle_other 2.468 r_scbond_it 2.199
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.968 r_dihedral_angle_4_deg 23.221 r_dihedral_angle_3_deg 18.216 r_dihedral_angle_1_deg 7.547 r_long_range_B_refined 6.399 r_long_range_B_other 6.322 r_scangle_other 3.334 r_mcangle_it 2.47 r_mcangle_other 2.468 r_scbond_it 2.199 r_scbond_other 2.19 r_angle_refined_deg 1.995 r_mcbond_it 1.807 r_mcbond_other 1.802 r_angle_other_deg 1.521 r_chiral_restr 0.093 r_bond_refined_d 0.018 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 908 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALEPACK data scaling MOLREP phasing