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Crystal Structure of VPS4B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 300 Ammonium Sulfate, HEPES, NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K, pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.5 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.058 α = 90 b = 88.058 β = 90 c = 112.574 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 ADSC QUANTUM 315 2003-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 ALS 8.3.1
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 2.8 76.6 99.3 0.058 0.058 9.7 10.9 12140 47.85
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) 2.8 2.87 99.3 0.285 0.285 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT NONE 2.8 76.7 10917 10917 1190 98.8 0.199 0.192 0.1926 0.26 0.2567 RANDOM 47.85
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] 1 0.5 1 -1.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.002 r_dihedral_angle_3_deg 20.641 r_dihedral_angle_4_deg 16.405 r_dihedral_angle_1_deg 6.41 r_scangle_it 3.804 r_scbond_it 2.294 r_angle_refined_deg 1.723 r_mcangle_it 1.686 r_mcbond_it 0.987 r_nbtor_refined 0.325
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.002 r_dihedral_angle_3_deg 20.641 r_dihedral_angle_4_deg 16.405 r_dihedral_angle_1_deg 6.41 r_scangle_it 3.804 r_scbond_it 2.294 r_angle_refined_deg 1.723 r_mcangle_it 1.686 r_mcbond_it 0.987 r_nbtor_refined 0.325 r_symmetry_vdw_refined 0.244 r_nbd_refined 0.242 r_xyhbond_nbd_refined 0.195 r_symmetry_hbond_refined 0.173 r_chiral_restr 0.11 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2508 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling SOLVE phasing