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Crystal Structure of Fission Yeast Arp2/3 Complex Lacking the Arp2 Subunit
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K8K PDB entry 1k8k
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 277 750 mM ammonium sulfate
50 mM sodium citrate
7 % glycerol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 5.17 76.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 218.967 α = 90 b = 218.967 β = 90 c = 315.049 γ = 90
Symmetry Space Group P 42 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 100 IMAGE PLATE MARRESEARCH 2005-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.10 NSLS X29A
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 3.78 29 98.9 0.198 9.5 73308 72502 2 2
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 3.775 3.872 92.1 0.495 2.6
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1k8k 3.78 29 73308 72502 3847 98.94 0.32469 0.3237 0.34367 RANDOM 74.74
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] 0.22 0.22 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.884 r_dihedral_angle_3_deg 18.758 r_dihedral_angle_4_deg 14.899 r_dihedral_angle_1_deg 5.152 r_scangle_it 1.505 r_angle_refined_deg 1.042 r_scbond_it 0.845 r_mcangle_it 0.797 r_mcbond_it 0.433 r_symmetry_vdw_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.884 r_dihedral_angle_3_deg 18.758 r_dihedral_angle_4_deg 14.899 r_dihedral_angle_1_deg 5.152 r_scangle_it 1.505 r_angle_refined_deg 1.042 r_scbond_it 0.845 r_mcangle_it 0.797 r_mcbond_it 0.433 r_symmetry_vdw_refined 0.323 r_nbtor_refined 0.305 r_symmetry_hbond_refined 0.247 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18643 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASES phasing