X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4LZD 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52980.1 M HEPES pH 7.5, 1.5 M Li2SO4
Crystal Properties
Matthews coefficientSolvent content
2.4750.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 124.989α = 90
b = 124.989β = 90
c = 50.618γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2018-04-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE TPS 05A1.0NSRRCTPS 05A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)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
11.723099.90.01548.814.143294
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.721.781000.0938.313.9

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 REPLACEMENTTHROUGHOUT4LZD1.723041058218099.810.192990.191460.22215RANDOM20.151
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]
-0.04-0.040.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.45
r_dihedral_angle_4_deg20.199
r_dihedral_angle_3_deg11.87
r_long_range_B_refined5.17
r_dihedral_angle_1_deg4.98
r_long_range_B_other4.948
r_scangle_other1.546
r_angle_refined_deg1.392
r_mcangle_it1.231
r_mcangle_other1.231
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.45
r_dihedral_angle_4_deg20.199
r_dihedral_angle_3_deg11.87
r_long_range_B_refined5.17
r_dihedral_angle_1_deg4.98
r_long_range_B_other4.948
r_scangle_other1.546
r_angle_refined_deg1.392
r_mcangle_it1.231
r_mcangle_other1.231
r_scbond_it0.947
r_scbond_other0.929
r_angle_other_deg0.921
r_mcbond_it0.71
r_mcbond_other0.71
r_chiral_restr0.078
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms2579
Nucleic Acid Atoms
Solvent Atoms349
Heterogen Atoms63

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing