1Z2X

Crystal structure of mouse Vps29


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
2.551.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.912α = 90
b = 68.321β = 106.98
c = 60.166γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATEMARRESEARCH2003-08-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.541

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.23099.40.0690.0816.83.8214206.325.8
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)RedundancyNumber Unique Reflections (All)
12.22.399.40.2160.2526.33.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMIRTHROUGHOUT2.222020185109199.520.175910.173050.22765RANDOM25.347
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
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg8.231
r_scangle_it4.067
r_scbond_it2.506
r_angle_refined_deg1.829
r_mcangle_it1.771
r_mcbond_it0.964
r_angle_other_deg0.939
r_nbd_other0.248
r_symmetry_vdw_other0.238
r_nbd_refined0.209
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg8.231
r_scangle_it4.067
r_scbond_it2.506
r_angle_refined_deg1.829
r_mcangle_it1.771
r_mcbond_it0.964
r_angle_other_deg0.939
r_nbd_other0.248
r_symmetry_vdw_other0.238
r_nbd_refined0.209
r_symmetry_vdw_refined0.175
r_xyhbond_nbd_refined0.169
r_chiral_restr0.126
r_symmetry_hbond_refined0.122
r_nbtor_other0.09
r_bond_refined_d0.019
r_gen_planes_other0.011
r_gen_planes_refined0.009
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 Atoms272
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
CCP4data scaling
SHARPphasing