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Crystal structure of mouse Vps29
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 0.1M Tris, 0.2M NaCl, 20% PEG3000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.5 51.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.912 α = 90 b = 68.321 β = 106.98 c = 60.166 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 IMAGE PLATE MARRESEARCH 2003-08-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.541
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 2.2 30 99.4 0.069 0.08 16.8 3.8 21420 6.3 25.8
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) 1 2.2 2.3 99.4 0.216 0.252 6.3 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MIR THROUGHOUT 2.22 20 20185 1091 99.52 0.17591 0.17305 0.1863 0.22765 0.239 RANDOM 25.347
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] 1.24 -1.42 -1.64 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.231 r_scangle_it 4.067 r_scbond_it 2.506 r_angle_refined_deg 1.829 r_mcangle_it 1.771 r_mcbond_it 0.964 r_angle_other_deg 0.939 r_nbd_other 0.248 r_symmetry_vdw_other 0.238 r_nbd_refined 0.209
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.231 r_scangle_it 4.067 r_scbond_it 2.506 r_angle_refined_deg 1.829 r_mcangle_it 1.771 r_mcbond_it 0.964 r_angle_other_deg 0.939 r_nbd_other 0.248 r_symmetry_vdw_other 0.238 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.175 r_xyhbond_nbd_refined 0.169 r_chiral_restr 0.126 r_symmetry_hbond_refined 0.122 r_nbtor_other 0.09 r_bond_refined_d 0.019 r_gen_planes_other 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 2892 Nucleic Acid Atoms Solvent Atoms 272 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CCP4 data scaling SHARP phasing