4BX9

Human Vps33A in complex with a fragment of human Vps16


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6293CRYSTALS WERE GROWN IN SITTING DROPS AT 20C. VPS33A:VPS16 COMPLEX (200 NL; A280 = 7.13, APPROX. 8.7 MG/ML) WAS MIXED 1:1 WITH RESERVOIR SOLUTION AND EQUILIBRATED AGAINST 80 UL RESERVOIRS CONTAINING 4% TACSIMATE PH 6.0, 12% PEG 3350 (HAMPTON RESEARCH). CRYSTALS WERE CRYOPROTECTED BY BRIEF IMMERSION IN RESERVOIR SOLUTION SUPPLEMENTED WITH 30% ETHYLENE GLYCOL AND CRYO-COOLED BY PLUNGING INTO LIQUID NITROGEN.
Crystal Properties
Matthews coefficientSolvent content
3.6466.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.41α = 90
b = 128.41β = 90
c = 263.36γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2MTOROIDAL2012-05-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-1DiamondI04-1

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
12.687.81000.1116.815.268560-376.138
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)
12.62.721001.312.114

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 REPLACEMENTTHROUGHOUTPDB ENTRY 4BX82.685.8465003346599.980.177620.175940.21024RANDOM70.508
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]
-0.75-0.751.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.529
r_dihedral_angle_4_deg19.91
r_dihedral_angle_3_deg16.432
r_dihedral_angle_1_deg6.239
r_angle_refined_deg1.756
r_angle_other_deg1.092
r_chiral_restr0.094
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.529
r_dihedral_angle_4_deg19.91
r_dihedral_angle_3_deg16.432
r_dihedral_angle_1_deg6.239
r_angle_refined_deg1.756
r_angle_other_deg1.092
r_chiral_restr0.094
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d0.005
r_gen_planes_other0.005
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 Atoms9973
Nucleic Acid Atoms
Solvent Atoms195
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing