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Crystal structure of mouse Vps29 complexed with Mn2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z2X
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 2.6 52.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.914 α = 90 b = 68.953 β = 106.65 c = 60.519 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 CCD ADSC QUANTUM 4 2004-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 0.87 SRS PX9.6
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 57 97.6 0.07 0.083 12.9 3.5 30024 3.7 26.1
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) 1 2 2.1 97.6 0.441 0.525 3.7 3.4
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 1Z2X 2 20 27724 1486 97.44 0.17939 0.17619 0.1842 0.23742 0.2411 RANDOM 27.858
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] -0.34 -1.93 -0.29 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.664 r_scangle_it 5.427 r_scbond_it 3.459 r_mcangle_it 2.58 r_angle_refined_deg 2.134 r_mcbond_it 1.432 r_angle_other_deg 1.073 r_symmetry_vdw_other 0.322 r_symmetry_vdw_refined 0.306 r_xyhbond_nbd_refined 0.284
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.664 r_scangle_it 5.427 r_scbond_it 3.459 r_mcangle_it 2.58 r_angle_refined_deg 2.134 r_mcbond_it 1.432 r_angle_other_deg 1.073 r_symmetry_vdw_other 0.322 r_symmetry_vdw_refined 0.306 r_xyhbond_nbd_refined 0.284 r_nbd_other 0.261 r_chiral_restr 0.238 r_nbd_refined 0.223 r_symmetry_hbond_refined 0.147 r_nbtor_other 0.095 r_bond_refined_d 0.026 r_gen_planes_refined 0.011 r_gen_planes_other 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 316 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement CCP4 data scaling