6YS1

Crystal structure of FAP R451K mutant in the dark at 100K


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6YRU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5281PEG 4000 25-40%, Na citrate 100 mM, spermidine 10mM
Crystal Properties
Matthews coefficientSolvent content
2.9458.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.62α = 90
b = 102.78β = 90
c = 155.83γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2018-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.966ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)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
11.649099.50.0720.0830.99812.224.2328764428.854
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.641.7599.50.8530.9840.5371.524.041

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6YRU1.6446.40187633434199.4680.1670.16610.192122.878
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]
0.818-0.26-0.557
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.961
r_dihedral_angle_4_deg16.172
r_dihedral_angle_3_deg14.267
r_dihedral_angle_1_deg6.959
r_lrange_it5.612
r_lrange_other5.522
r_scangle_it4.761
r_scangle_other4.76
r_scbond_it3.233
r_scbond_other3.233
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.961
r_dihedral_angle_4_deg16.172
r_dihedral_angle_3_deg14.267
r_dihedral_angle_1_deg6.959
r_lrange_it5.612
r_lrange_other5.522
r_scangle_it4.761
r_scangle_other4.76
r_scbond_it3.233
r_scbond_other3.233
r_mcangle_it2.387
r_mcangle_other2.387
r_angle_refined_deg1.798
r_mcbond_it1.791
r_mcbond_other1.785
r_angle_other_deg1.527
r_symmetry_xyhbond_nbd_refined0.475
r_nbd_other0.254
r_nbd_refined0.207
r_symmetry_nbd_refined0.2
r_symmetry_nbd_other0.191
r_nbtor_refined0.17
r_xyhbond_nbd_refined0.153
r_chiral_restr0.09
r_symmetry_nbtor_other0.087
r_bond_refined_d0.012
r_gen_planes_refined0.012
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4254
Nucleic Acid Atoms
Solvent Atoms365
Heterogen Atoms106

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing