2H16

Structure of human ADP-ribosylation factor-like 5 (ARL5)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZJ6pdb entry 1zj6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529120% PEG3350, 0.2M diammomium citrate, 5mM Tris, pH 7.5, vapor diffusion, sitting drop, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.8857.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.624α = 90
b = 94.624β = 90
c = 214.836γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102005-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.0000APS17-ID

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
125093.70.05315.711.162818
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)
22.0751.90.2664.6

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTpdb entry 1zj623062682192093.9390.2050.20410.2339Thin shells27.459
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]
0.7280.728-1.456
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.521
r_dihedral_angle_4_deg17.958
r_dihedral_angle_3_deg11.856
r_dihedral_angle_1_deg5.03
r_scangle_it4.161
r_mcangle_it3.888
r_scbond_it2.977
r_mcbond_it2.812
r_angle_refined_deg1.384
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.521
r_dihedral_angle_4_deg17.958
r_dihedral_angle_3_deg11.856
r_dihedral_angle_1_deg5.03
r_scangle_it4.161
r_mcangle_it3.888
r_scbond_it2.977
r_mcbond_it2.812
r_angle_refined_deg1.384
r_nbtor_refined0.3
r_nbd_refined0.193
r_symmetry_vdw_refined0.184
r_symmetry_hbond_refined0.167
r_xyhbond_nbd_refined0.125
r_chiral_restr0.092
r_bond_refined_d0.015
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4836
Nucleic Acid Atoms
Solvent Atoms270
Heterogen Atoms140

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ARP/wARPmodel building
MolProbitymodel building