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Crystal structure of ADP RIBOSYLATION FACTOR-LIKE GTP BINDING PROTEIN /Small COPII coat GTPase SAR1 from Encephalitozoon cuniculi in complex with GDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model MR rosetta based on top 16 HHPRED results
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 RigakuReagents JCSG+ screen, condition B10 + 10% RigakuReagents ADDIT G7: 50% (V/V) PEG 200, 200mM MgCl2, 100mM Na-cacodylate pH 6.5 + 10mM spermine: EncuA.00324.a.MB1.PW30297 at 12mg/ml + 5mM GDP: cryo: 20% EG: tray: 225442g7: puck txl1-11.
Crystal Properties Matthews coefficient Solvent content 3.24 62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.19 α = 90 b = 65.19 β = 90 c = 307.71 γ = 90
Symmetry Space Group P 43 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 300 mm CCD 2011-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9795 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 2.4 50 99.7 0.053 0.057 0.999 21.49 7.025 27225 60.444
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.46 99.9 0.558 0.6 0.933 3.29 7.352
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE MR rosetta based on top 16 HHPRED results 2.4 45.59 1.34 27104 1933 99.7 0.1843 0.1804 0.1889 0.235 0.2408 0 66.57
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 f_dihedral_angle_d 18.3235 f_angle_d 0.6768 f_chiral_restr 0.0481 f_plane_restr 0.0043 f_bond_d 0.0042
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3511 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 21
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction MR-Rosetta phasing