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The crystal structure of ASAP3 in complex with Arf6 in transition state soaked with Calcium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LVQ PDB ENTRY 3LVQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 13% PEG 8000, 150mM Magnesium Acetate, 100mM MOPS(pH 7.5); Crystals were then soaked in 30mM CaCl2 , VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.8 56.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.45 α = 90 b = 146.45 β = 90 c = 49.62 γ = 120
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 2009-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.3838 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.38 29.46 99.7 0.101 0.08 19 5.85 8310 8310 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3.38 3.5 99.5 0.575 0.676 3.5 5.8 1657
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 PDB ENTRY 3LVQ 3.38 29.46 8294 437 100 0.21095 0.20746 0.1938 0.28129 0.27 RANDOM 125.397
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] -6.75 -3.38 -6.75 10.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.465 r_dihedral_angle_3_deg 17.901 r_dihedral_angle_4_deg 13.86 r_dihedral_angle_1_deg 5.473 r_angle_refined_deg 1.058 r_scangle_it 0.813 r_scbond_it 0.446 r_mcangle_it 0.405 r_nbtor_refined 0.299 r_mcbond_it 0.223
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.465 r_dihedral_angle_3_deg 17.901 r_dihedral_angle_4_deg 13.86 r_dihedral_angle_1_deg 5.473 r_angle_refined_deg 1.058 r_scangle_it 0.813 r_scbond_it 0.446 r_mcangle_it 0.405 r_nbtor_refined 0.299 r_mcbond_it 0.223 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.195 r_xyhbond_nbd_refined 0.137 r_metal_ion_refined 0.113 r_chiral_restr 0.076 r_bond_refined_d 0.006 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3257 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 35
Software Software Software Name Purpose ProDC data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling