6YRU

Crystal structure of FAP in the dark at 100K


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5NCC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5281PEG 4000 25-40%, Na citrate 100 mM, spermidine 10mM
Crystal Properties
Matthews coefficientSolvent content
2.9858.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.69α = 90
b = 103.57β = 90
c = 155.95γ = 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
11.788699.30.0860.0960.99811.024.7276924034.226
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)
11.781.999.41.1321.2690.5121.034.838

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-VALUE5NCC1.7846.50369195343199.2130.1740.17210.202130.186
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]
0.730.486-1.216
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.381
r_dihedral_angle_4_deg15.19
r_dihedral_angle_3_deg12.788
r_lrange_it10.061
r_lrange_other9.773
r_dihedral_angle_1_deg7.482
r_scangle_it6.17
r_scangle_other6.169
r_scbond_other4.613
r_scbond_it4.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.381
r_dihedral_angle_4_deg15.19
r_dihedral_angle_3_deg12.788
r_lrange_it10.061
r_lrange_other9.773
r_dihedral_angle_1_deg7.482
r_scangle_it6.17
r_scangle_other6.169
r_scbond_other4.613
r_scbond_it4.61
r_mcangle_other3.218
r_mcangle_it3.216
r_mcbond_it2.346
r_mcbond_other2.339
r_angle_refined_deg1.661
r_angle_other_deg1.468
r_symmetry_nbd_refined0.278
r_nbd_other0.238
r_xyhbond_nbd_refined0.235
r_nbd_refined0.202
r_symmetry_xyhbond_nbd_refined0.197
r_symmetry_nbd_other0.185
r_nbtor_refined0.167
r_symmetry_xyhbond_nbd_other0.098
r_symmetry_nbtor_other0.082
r_chiral_restr0.077
r_bond_refined_d0.011
r_gen_planes_refined0.011
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 Atoms525
Heterogen Atoms93

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction