X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3P5Q 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE6.742983.2M Na/K phosphate buffer
Crystal Properties
Matthews coefficientSolvent content
2.1843.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.338α = 90
b = 53.338β = 90
c = 190.647γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 300K2017-11-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.1550930.0430.98214.221.426737
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.180.0250.983

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 REPLACEMENTTHROUGHOUT3P5Q2.1546.5925338139492.560.220060.216460.28583RANDOM26.497
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]
-0.05-0.050.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.092
r_dihedral_angle_4_deg19.716
r_dihedral_angle_3_deg15.741
r_dihedral_angle_1_deg6.653
r_long_range_B_refined5.001
r_long_range_B_other4.994
r_mcangle_other2.841
r_mcangle_it2.84
r_scangle_other2.733
r_mcbond_it1.805
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.092
r_dihedral_angle_4_deg19.716
r_dihedral_angle_3_deg15.741
r_dihedral_angle_1_deg6.653
r_long_range_B_refined5.001
r_long_range_B_other4.994
r_mcangle_other2.841
r_mcangle_it2.84
r_scangle_other2.733
r_mcbond_it1.805
r_mcbond_other1.803
r_scbond_it1.691
r_scbond_other1.691
r_angle_refined_deg1.381
r_angle_other_deg0.909
r_chiral_restr0.069
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_gen_planes_other0.004
r_bond_other_d0.001
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 Atoms4324
Nucleic Acid Atoms
Solvent Atoms94
Heterogen Atoms211

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000data collection
PHASERphasing