6YRZ

Crystal structure of FAP et pH 8.5 after illumination at 150K


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5281PEG 4000 25-40%, Na citrate 100 mM, spermidine 10mM
Crystal Properties
Matthews coefficientSolvent content
3.0459.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.47α = 90
b = 104.56β = 90
c = 156.9γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray150PIXELDECTRIS EIGER X 4M2019-09-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.979SOLEILPROXIMA 1

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
11.828799.70.0860.0890.99918.3813.5186626737.236
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)
11.821.9398.21.0381.0780.8162.0913.489

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-VALUE6YRU1.82446.81966267331299.6660.160.15830.188133.727
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]
0.011-0.0240.013
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.17
r_dihedral_angle_4_deg16.822
r_dihedral_angle_3_deg13.923
r_dihedral_angle_1_deg7.397
r_lrange_it6.887
r_lrange_other6.784
r_scangle_it5.756
r_scangle_other5.755
r_scbond_it3.947
r_scbond_other3.946
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.17
r_dihedral_angle_4_deg16.822
r_dihedral_angle_3_deg13.923
r_dihedral_angle_1_deg7.397
r_lrange_it6.887
r_lrange_other6.784
r_scangle_it5.756
r_scangle_other5.755
r_scbond_it3.947
r_scbond_other3.946
r_mcangle_it3.632
r_mcangle_other3.632
r_mcbond_it2.975
r_mcbond_other2.973
r_angle_refined_deg1.728
r_angle_other_deg1.465
r_symmetry_xyhbond_nbd_refined0.311
r_symmetry_nbd_refined0.285
r_nbd_other0.263
r_symmetry_xyhbond_nbd_other0.215
r_nbd_refined0.208
r_symmetry_nbd_other0.187
r_xyhbond_nbd_refined0.176
r_nbtor_refined0.168
r_chiral_restr0.089
r_symmetry_nbtor_other0.083
r_bond_refined_d0.012
r_gen_planes_refined0.012
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4216
Nucleic Acid Atoms
Solvent Atoms440
Heterogen Atoms109

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing