6YS2

Crystal structure of FAP R451A 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
2.6553.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.95α = 90
b = 60.82β = 90
c = 180.15γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2018-09-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97625ESRFID29

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
11.978699.50.1340.150.9968.564.8484646333.757
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)
11.972.09991.011.1310.5681.444.871

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-VALUE6YRU1.9749.37546460242599.4480.1840.1820.228733.043
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]
-1.2251.1640.061
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.659
r_dihedral_angle_4_deg16.682
r_dihedral_angle_3_deg14.028
r_dihedral_angle_1_deg7.718
r_lrange_it6.57
r_lrange_other6.496
r_scangle_it4.611
r_scangle_other4.61
r_mcangle_other3.552
r_mcangle_it3.551
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.659
r_dihedral_angle_4_deg16.682
r_dihedral_angle_3_deg14.028
r_dihedral_angle_1_deg7.718
r_lrange_it6.57
r_lrange_other6.496
r_scangle_it4.611
r_scangle_other4.61
r_mcangle_other3.552
r_mcangle_it3.551
r_scbond_it3.054
r_scbond_other3.054
r_mcbond_it2.552
r_mcbond_other2.544
r_angle_refined_deg1.618
r_angle_other_deg1.332
r_nbd_other0.223
r_nbd_refined0.196
r_symmetry_nbd_other0.189
r_xyhbond_nbd_refined0.179
r_symmetry_xyhbond_nbd_refined0.177
r_nbtor_refined0.163
r_symmetry_nbd_refined0.152
r_symmetry_xyhbond_nbd_other0.09
r_symmetry_nbtor_other0.079
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4192
Nucleic Acid Atoms
Solvent Atoms314
Heterogen Atoms93

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing