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Crystal structure of ldtMt2 at 1.79 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VYN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 20% PEG5000MME, 0.2mM Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.91 57.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.644 α = 89.04 b = 75.534 β = 89.96 c = 94.143 γ = 92.76
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 MIRRORS 2015-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.979 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.7 50 97.3 0.068 0.078 0.041 7.6 3.7 153919
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 95.7 0.8 0.544 0.577 3.5 8817
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 3VYN 1.79 50 144115 7371 94.72 0.1716 0.1696 0.1798 0.21 0.2181 RANDOM 17.48
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] 0.17 0.04 0.1 -0.25 -0.07 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.349 r_dihedral_angle_4_deg 18.412 r_dihedral_angle_3_deg 12.948 r_dihedral_angle_1_deg 6.364 r_mcangle_it 2.398 r_angle_refined_deg 1.991 r_mcbond_it 1.566 r_mcbond_other 1.566 r_angle_other_deg 1.103 r_chiral_restr 0.154
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.349 r_dihedral_angle_4_deg 18.412 r_dihedral_angle_3_deg 12.948 r_dihedral_angle_1_deg 6.364 r_mcangle_it 2.398 r_angle_refined_deg 1.991 r_mcbond_it 1.566 r_mcbond_other 1.566 r_angle_other_deg 1.103 r_chiral_restr 0.154 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10558 Nucleic Acid Atoms Solvent Atoms 1827 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection HKL-2000 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction