4BX8

Human Vps33A


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293CRYSTALS WERE GROWN IN SITTING DROPS AT 20 C. VPS33A-HIS10 (200 NL; 3.2 MG/ML) WAS EQUILIBRATED AGAINST 80 UL RESERVOIRS CONTAINING 14.3-12.8% (W/V) PEG 3350 AND 143-128 MM AMMONIUM ACETATE (HAMPTON RESEARCH). CRYSTALS WERE CRYOPROTECTED BY ADDING RESERVOIR SOLUTION SUPPLEMENTED WITH 30% (V/V) ETHYLENE GLYCOL TO THE MOTHER LIQUOR IMMEDIATELY BEFORE HARVESTING AND CRYO-COOLING BY PLUNGING INTO LIQUID NITROGEN. ANNEALING BY BLOCKING THE CRYOSTREAM FOR 5 S GREATLY ENHANCED THE DIFFRACTION OF VPS33A CRYSTALS.
Crystal Properties
Matthews coefficientSolvent content
2.4349.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.47α = 90
b = 125.01β = 115.33
c = 83.28γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MKIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING2011-05-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.464.596.90.099.53.549915-353.776
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.4997.80.771.73.6

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 DIFFRACTIONMIRASTHROUGHOUTNONE2.464.6147789210396.450.199140.197210.24377RANDOM58.244
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]
-4.90.194.650.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.862
r_dihedral_angle_4_deg18.117
r_dihedral_angle_3_deg14.568
r_dihedral_angle_1_deg6.315
r_angle_refined_deg1.531
r_angle_other_deg0.979
r_chiral_restr0.081
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.862
r_dihedral_angle_4_deg18.117
r_dihedral_angle_3_deg14.568
r_dihedral_angle_1_deg6.315
r_angle_refined_deg1.531
r_angle_other_deg0.979
r_chiral_restr0.081
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d0.004
r_gen_planes_other0.004
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9062
Nucleic Acid Atoms
Solvent Atoms73
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing