X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JD0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.62940.2M AMMONIUM ACETATE, 0.1M SODIUM CITRATE, PH 5.6, 31% PEG 4000, PROTEIN CONC. 10 MG/ML, 5-10 MM INHIBITOR (STOCK SOLUTION WAS DISSOLVED IN 100% DMSO)
Crystal Properties
Matthews coefficientSolvent content
2.2445.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.76α = 90.02
b = 74.76β = 74.32
c = 76.23γ = 90
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-09-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.918400BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.8974.7683.20.0944.61.86481021.92
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.891.9982.80.43321.8

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1JD01.8974.7661577323283.210.167780.164760.22458RANDOM22.388
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]
-0.32-0.180.641.820.3-0.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.611
r_dihedral_angle_4_deg17.656
r_dihedral_angle_3_deg14.485
r_dihedral_angle_1_deg7.975
r_long_range_B_refined5.274
r_long_range_B_other5.217
r_scangle_other3.877
r_mcangle_it2.694
r_mcangle_other2.694
r_scbond_it2.489
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.611
r_dihedral_angle_4_deg17.656
r_dihedral_angle_3_deg14.485
r_dihedral_angle_1_deg7.975
r_long_range_B_refined5.274
r_long_range_B_other5.217
r_scangle_other3.877
r_mcangle_it2.694
r_mcangle_other2.694
r_scbond_it2.489
r_scbond_other2.489
r_mcbond_it1.827
r_mcbond_other1.826
r_angle_refined_deg1.664
r_angle_other_deg1.379
r_chiral_restr0.077
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.003
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8338
Nucleic Acid Atoms
Solvent Atoms726
Heterogen Atoms112

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling