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2.8 A crystal structure of a Get3-Get4-Get5 intermediate complex from S.cerevisiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A37 3A37 and 3LKU experimental model PDB 3LKU 3A37 and 3LKU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 17% PEG 3350, 0.24 M Na citrate, and 30 mM TCEP
Crystal Properties Matthews coefficient Solvent content 2.76 55.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.96 α = 90 b = 238.05 β = 90 c = 52.19 γ = 90
Symmetry Space Group P 21 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 PSI PILATUS 6M 2012-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 1 SSRL BL12-2
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 2.8 29.8 97 0.06 8.3 3.3 34114
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 2.8 2.9 95.7 0.58 1.6 3.1
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 3A37 and 3LKU 2.8 29.8 32332 1710 96.17 0.2259 0.22404 0.2255 0.26161 0.2606 RANDOM 111.032
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] 5.29 -1.23 -4.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.574 r_dihedral_angle_4_deg 20.029 r_dihedral_angle_3_deg 17.384 r_long_range_B_other 13.185 r_long_range_B_refined 13.184 r_dihedral_angle_1_deg 6.251 r_mcangle_other 6.12 r_mcangle_it 6.118 r_scangle_other 5.119 r_mcbond_it 3.712
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.574 r_dihedral_angle_4_deg 20.029 r_dihedral_angle_3_deg 17.384 r_long_range_B_other 13.185 r_long_range_B_refined 13.184 r_dihedral_angle_1_deg 6.251 r_mcangle_other 6.12 r_mcangle_it 6.118 r_scangle_other 5.119 r_mcbond_it 3.712 r_mcbond_other 3.705 r_scbond_it 3.039 r_scbond_other 3.039 r_angle_refined_deg 1.697 r_angle_other_deg 1.033 r_chiral_restr 0.116 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.003 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 7741 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing Coot model building