☰ Navigation Tabs
mouse TDH in the apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YR9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 283 0.1 M Sodium HEPES, 10%(w/v) PEG 4000, 10%(v/v) 2-Propanol
Crystal Properties Matthews coefficient Solvent content 2.72 54.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.445 α = 90 b = 157.31 β = 97 c = 162.336 γ = 90
Symmetry Space Group P 1 21 1
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 315r 2014-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.979 SSRF BL17U
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 2.65 50 93.9 0.062 0.081 0.051 10.3 2.1 127736
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 2.65 2.74 94.6 0.387 0.508 0.325 0.845 2 12829
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 4YR9 2.65 44.35 118620 6300 91.49 0.2196 0.2169 0.217 0.2712 0.2683 RANDOM 65.471
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 33.215 r_dihedral_angle_3_deg 15.747 r_dihedral_angle_4_deg 15.14 r_dihedral_angle_1_deg 5.774 r_mcangle_it 3.229 r_mcbond_it 1.884 r_mcbond_other 1.884 r_angle_refined_deg 0.951 r_angle_other_deg 0.714 r_chiral_restr 0.052
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.215 r_dihedral_angle_3_deg 15.747 r_dihedral_angle_4_deg 15.14 r_dihedral_angle_1_deg 5.774 r_mcangle_it 3.229 r_mcbond_it 1.884 r_mcbond_other 1.884 r_angle_refined_deg 0.951 r_angle_other_deg 0.714 r_chiral_restr 0.052 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 27721 Nucleic Acid Atoms Solvent Atoms 70 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data collection PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing