X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5N4C 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2 M sodium acetate, 0.1 M Bis-Tris propane (pH 6.0-6.5) and 28% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.141.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.86α = 83.97
b = 113.43β = 82.09
c = 186.32γ = 76.93
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2020-01-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

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
11.9466.08397.60.0750.09517.32.5397483
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)
11.941.9796.60.9381.1950.3520.92.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5N4C1.9466.0833974211970197.5640.2140.21250.24142.824
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]
2.155-0.2820.290.025-2.063-2.352
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.153
r_dihedral_angle_4_deg15.92
r_dihedral_angle_3_deg13.918
r_lrange_other10.453
r_lrange_it10.446
r_scangle_it8.737
r_scangle_other8.736
r_dihedral_angle_1_deg6.984
r_scbond_it6.322
r_scbond_other6.322
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.153
r_dihedral_angle_4_deg15.92
r_dihedral_angle_3_deg13.918
r_lrange_other10.453
r_lrange_it10.446
r_scangle_it8.737
r_scangle_other8.736
r_dihedral_angle_1_deg6.984
r_scbond_it6.322
r_scbond_other6.322
r_mcangle_it6.314
r_mcangle_other6.314
r_mcbond_it4.77
r_mcbond_other4.77
r_angle_refined_deg1.367
r_angle_other_deg1.227
r_symmetry_xyhbond_nbd_refined0.286
r_symmetry_nbd_refined0.266
r_nbd_other0.263
r_nbd_refined0.196
r_symmetry_nbd_other0.175
r_nbtor_refined0.165
r_xyhbond_nbd_refined0.135
r_metal_ion_refined0.091
r_ncsr_local_group_210.084
r_ncsr_local_group_280.083
r_ncsr_local_group_170.082
r_ncsr_local_group_240.079
r_xyhbond_nbd_other0.077
r_ncsr_local_group_60.076
r_ncsr_local_group_220.076
r_ncsr_local_group_120.075
r_ncsr_local_group_260.075
r_symmetry_nbtor_other0.074
r_ncsr_local_group_200.074
r_ncsr_local_group_270.072
r_ncsr_local_group_70.07
r_ncsr_local_group_140.07
r_ncsr_local_group_180.07
r_ncsr_local_group_230.069
r_ncsr_local_group_250.069
r_ncsr_local_group_110.068
r_ncsr_local_group_130.067
r_ncsr_local_group_90.066
r_ncsr_local_group_160.066
r_ncsr_local_group_190.065
r_ncsr_local_group_50.064
r_ncsr_local_group_30.063
r_chiral_restr0.062
r_ncsr_local_group_150.062
r_ncsr_local_group_80.06
r_ncsr_local_group_100.059
r_ncsr_local_group_40.058
r_ncsr_local_group_10.055
r_ncsr_local_group_20.055
r_chiral_restr_other0.019
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_symmetry_xyhbond_nbd_other0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms46130
Nucleic Acid Atoms
Solvent Atoms898
Heterogen Atoms103

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing