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Crystal structure of Drosophila melanogaster Translin protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J1J PDB entry 1J1J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 2.0M ammonium sulfate, 2% MPD, 5% glycerol, 100mM MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 5.9 78.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.778 α = 90 b = 152.778 β = 90 c = 94.007 γ = 120
Symmetry Space Group P 62 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 IMAGE PLATE RIGAKU RAXIS IIC OSMIC mirror 2004-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 3.6 20 93.7 0.106 13.3 2.8 7311 7311 51
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) 3.6 3.79 91.4 0.412 2.8 3 1012
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1J1J 3.6 20 7311 7308 335 100 0.217 0.215 0.2046 0.249 0.2331 RANDOM 65.4
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] -4.16 -2.08 -4.16 6.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.079 r_dihedral_angle_3_deg 21.146 r_dihedral_angle_4_deg 20.632 r_dihedral_angle_1_deg 6.337 r_scangle_it 3.757 r_scbond_it 2.068 r_angle_refined_deg 1.804 r_mcangle_it 1.512 r_mcbond_it 0.78 r_nbtor_refined 0.338
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.079 r_dihedral_angle_3_deg 21.146 r_dihedral_angle_4_deg 20.632 r_dihedral_angle_1_deg 6.337 r_scangle_it 3.757 r_scbond_it 2.068 r_angle_refined_deg 1.804 r_mcangle_it 1.512 r_mcbond_it 0.78 r_nbtor_refined 0.338 r_nbd_refined 0.278 r_symmetry_vdw_refined 0.219 r_xyhbond_nbd_refined 0.185 r_chiral_restr 0.117 r_bond_refined_d 0.017 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1502 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing