6VSK

Crystal structure of the P-Rex1 DEP1 domain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1O7FPDB entry 1O7F

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293.150.1 M HEPES, pH 6.5, 45% w/v poly(acrylic acid sodium salt)2100
Crystal Properties
Matthews coefficientSolvent content
4.7674.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.152α = 90
b = 103.152β = 90
c = 67.981γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80PIXELDECTRIS PILATUS3 6M2018-11-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.0332APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)Rpim I (All)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
13.125099.30.1520.049198.44105
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.123.1795.40.6020.3160.7131.33

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 1O7F3.1219.62386221398.60.18550.18290.2332RANDOM105.74
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]
-0.18-0.09-0.180.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.839
r_dihedral_angle_3_deg19.909
r_dihedral_angle_1_deg9.487
r_dihedral_angle_4_deg9.04
r_angle_refined_deg1.796
r_angle_other_deg1.236
r_chiral_restr0.065
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.839
r_dihedral_angle_3_deg19.909
r_dihedral_angle_1_deg9.487
r_dihedral_angle_4_deg9.04
r_angle_refined_deg1.796
r_angle_other_deg1.236
r_chiral_restr0.065
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms750
Nucleic Acid Atoms
Solvent Atoms4
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing