1Z2W

Crystal structure of mouse Vps29 complexed with Mn2+


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52890.1M Tris, 0.2M NaCl, 20% PEG3000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.652.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.914α = 90
b = 68.953β = 106.65
c = 60.519γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 42004-06-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX9.60.87SRSPX9.6

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
125797.60.070.08312.93.5300243.726.1
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)RedundancyNumber Unique Reflections (All)
122.197.60.4410.5253.73.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1Z2X22027724148697.440.179390.176190.23742RANDOM27.858
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
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.664
r_scangle_it5.427
r_scbond_it3.459
r_mcangle_it2.58
r_angle_refined_deg2.134
r_mcbond_it1.432
r_angle_other_deg1.073
r_symmetry_vdw_other0.322
r_symmetry_vdw_refined0.306
r_xyhbond_nbd_refined0.284
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.664
r_scangle_it5.427
r_scbond_it3.459
r_mcangle_it2.58
r_angle_refined_deg2.134
r_mcbond_it1.432
r_angle_other_deg1.073
r_symmetry_vdw_other0.322
r_symmetry_vdw_refined0.306
r_xyhbond_nbd_refined0.284
r_nbd_other0.261
r_chiral_restr0.238
r_nbd_refined0.223
r_symmetry_hbond_refined0.147
r_nbtor_other0.095
r_bond_refined_d0.026
r_gen_planes_refined0.011
r_gen_planes_other0.009
r_bond_other_d0.002
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 AtomsNumber
Protein Atoms2892
Nucleic Acid Atoms
Solvent Atoms316
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
CCP4data scaling