6HH4 | pdb_00006hh4

ADP-ribosylserine hydrolase ARH3 of Latimeria chalumnae in complex with ADP-ribosyl-L-arginine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FOZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.6293.15200 MM AMMONIUM ACETATE, 25 % (W/V), PEG4000, 100 MM CITRATE PH 5.6
Crystal Properties
Matthews coefficientSolvent content
2.3948.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.145α = 90
b = 96.642β = 90
c = 105.908γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-08-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.9686DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim 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
11.6671.391000.0890.1010.0470.9979.98.382067
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.661.71001.5241.7330.8090.6768.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2FOZ1.6671.3977918403099.810.169650.168550.180.189940.2RANDOM32.064
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]
-1.33-1.73.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.788
r_dihedral_angle_4_deg18.297
r_dihedral_angle_3_deg13.074
r_dihedral_angle_1_deg5.479
r_long_range_B_refined4.552
r_long_range_B_other4.481
r_scangle_other2.597
r_mcangle_it1.818
r_mcangle_other1.817
r_scbond_it1.676
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.788
r_dihedral_angle_4_deg18.297
r_dihedral_angle_3_deg13.074
r_dihedral_angle_1_deg5.479
r_long_range_B_refined4.552
r_long_range_B_other4.481
r_scangle_other2.597
r_mcangle_it1.818
r_mcangle_other1.817
r_scbond_it1.676
r_scbond_other1.675
r_angle_refined_deg1.531
r_mcbond_it1.142
r_mcbond_other1.14
r_angle_other_deg1.063
r_chiral_restr0.09
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5039
Nucleic Acid Atoms
Solvent Atoms521
Heterogen Atoms118

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
DIALSdata scaling
PHASERphasing