2H17

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Z6Ypdb entry 1z6y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72912.0M sodium formate, 0.1M BTP, pH 7.0, vapor diffusion, sitting drop, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
1.9837.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.047α = 90
b = 48.772β = 90
c = 85.711γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102005-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID0.97895APS17-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
11.728.7298.90.05511.76.918505
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)
1.71.7697.60.4755.6

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 1z6y1.728.721843093898.8890.1880.18560.2267random17.799
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]
-0.62-0.51.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.205
r_dihedral_angle_4_deg16.392
r_dihedral_angle_3_deg11.122
r_dihedral_angle_1_deg5.883
r_scangle_it4.822
r_mcangle_it3.723
r_scbond_it3.204
r_mcbond_it3.106
r_angle_refined_deg1.469
r_angle_other_deg1.052
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.205
r_dihedral_angle_4_deg16.392
r_dihedral_angle_3_deg11.122
r_dihedral_angle_1_deg5.883
r_scangle_it4.822
r_mcangle_it3.723
r_scbond_it3.204
r_mcbond_it3.106
r_angle_refined_deg1.469
r_angle_other_deg1.052
r_mcbond_other0.728
r_symmetry_vdw_other0.345
r_nbd_refined0.213
r_nbd_other0.206
r_nbtor_refined0.171
r_symmetry_hbond_refined0.168
r_xyhbond_nbd_refined0.156
r_symmetry_vdw_refined0.114
r_chiral_restr0.094
r_nbtor_other0.077
r_bond_refined_d0.017
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1314
Nucleic Acid Atoms
Solvent Atoms64
Heterogen Atoms31

Software

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