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Structure of the C-terminal Sec63 unit of yeast Brr2, P41212 Form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IM1 PDB ID 3IM1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 100mM sodium cacodylate, pH 6.0, 100mM Li2SO4, 15 % PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.82 56.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.09 α = 90 b = 104.09 β = 90 c = 77.373 γ = 90
Symmetry Space Group P 41 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 CCD MARMOSAIC 225 mm CCD mirrors 2006-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.05 MPG/DESY, HAMBURG BW6
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.99 30 99.2 0.1 13.7 3.1 29754 29516 1 1 35.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.12 99.3 0.56 1.7 3.2 4644
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 (All) 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 ID 3IM1 1.99 20 28257 27975 1503 99 0.19009 0.19009 0.18765 0.187 0.23655 0.233 RANDOM 37.145
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] 0.2 0.2 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.086 r_dihedral_angle_4_deg 19.482 r_dihedral_angle_3_deg 15.499 r_dihedral_angle_1_deg 5.571 r_scangle_it 1.539 r_angle_refined_deg 1.192 r_scbond_it 0.972 r_mcangle_it 0.615 r_mcbond_it 0.381 r_nbtor_refined 0.289
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.086 r_dihedral_angle_4_deg 19.482 r_dihedral_angle_3_deg 15.499 r_dihedral_angle_1_deg 5.571 r_scangle_it 1.539 r_angle_refined_deg 1.192 r_scbond_it 0.972 r_mcangle_it 0.615 r_mcbond_it 0.381 r_nbtor_refined 0.289 r_symmetry_hbond_refined 0.181 r_nbd_refined 0.18 r_symmetry_vdw_refined 0.169 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2560 Nucleic Acid Atoms Solvent Atoms 352 Heterogen Atoms 13
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling