6YRV

Crystal structure of FAP after illumination 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
3.0159.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.96α = 90
b = 103.86β = 90
c = 156.3γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2018-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97372ESRFID29

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
11.9486.51000.1060.1160.99811.626.5855460034.131
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)
11.941.991000.780.8490.7242.236.525

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-VALUE6YRU1.948654459282899.960.1670.16510.203329.774
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]
0.9840.631-1.615
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.16
r_dihedral_angle_4_deg16.441
r_dihedral_angle_3_deg14.333
r_lrange_it12.909
r_lrange_other12.39
r_dihedral_angle_1_deg7.441
r_scangle_it5.02
r_scangle_other5.02
r_scbond_it3.416
r_scbond_other3.416
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.16
r_dihedral_angle_4_deg16.441
r_dihedral_angle_3_deg14.333
r_lrange_it12.909
r_lrange_other12.39
r_dihedral_angle_1_deg7.441
r_scangle_it5.02
r_scangle_other5.02
r_scbond_it3.416
r_scbond_other3.416
r_mcangle_it3.372
r_mcangle_other3.372
r_mcbond_it2.452
r_mcbond_other2.45
r_angle_refined_deg1.697
r_angle_other_deg1.443
r_symmetry_nbd_refined0.29
r_symmetry_xyhbond_nbd_refined0.255
r_nbd_other0.228
r_xyhbond_nbd_refined0.222
r_nbd_refined0.207
r_symmetry_nbd_other0.185
r_nbtor_refined0.164
r_symmetry_xyhbond_nbd_other0.091
r_chiral_restr0.084
r_symmetry_nbtor_other0.082
r_gen_planes_refined0.012
r_bond_refined_d0.011
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4267
Nucleic Acid Atoms
Solvent Atoms524
Heterogen Atoms93

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing