X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NG3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52930.1 M Tris-HCl pH8.5, 0.2 M KBr, 8 % PEG 550 MME and 8 % PEG 20000
Crystal Properties
Matthews coefficientSolvent content
3.3959.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.386α = 89.853
b = 107.803β = 89.989
c = 134.754γ = 83.575
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2021-04-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE TPS 05A1NSRRCTPS 05A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.933097.90.0430.0480.02135.85.3424903
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)
11.93296.50.280.3110.1350.9625.95.3

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-VALUE1ng31.9329.7184248822132097.7330.1930.19210.208323.627
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]
0.079-0.0710.017-0.058-0.112
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.737
r_dihedral_angle_4_deg16.642
r_dihedral_angle_3_deg14.981
r_dihedral_angle_1_deg6.711
r_lrange_it5.25
r_lrange_other4.999
r_scangle_it3.274
r_scangle_other3.274
r_mcangle_it2.446
r_mcangle_other2.446
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.737
r_dihedral_angle_4_deg16.642
r_dihedral_angle_3_deg14.981
r_dihedral_angle_1_deg6.711
r_lrange_it5.25
r_lrange_other4.999
r_scangle_it3.274
r_scangle_other3.274
r_mcangle_it2.446
r_mcangle_other2.446
r_scbond_it2.025
r_scbond_other2.024
r_mcbond_it1.569
r_mcbond_other1.569
r_angle_refined_deg1.371
r_angle_other_deg1.308
r_nbd_other0.271
r_symmetry_nbd_refined0.262
r_nbd_refined0.193
r_symmetry_nbd_other0.183
r_symmetry_xyhbond_nbd_refined0.166
r_xyhbond_nbd_refined0.155
r_nbtor_refined0.154
r_symmetry_xyhbond_nbd_other0.1
r_symmetry_nbtor_other0.08
r_ncsr_local_group_300.072
r_chiral_restr0.068
r_ncsr_local_group_280.066
r_ncsr_local_group_20.065
r_ncsr_local_group_60.064
r_ncsr_local_group_150.064
r_ncsr_local_group_80.063
r_ncsr_local_group_170.063
r_ncsr_local_group_330.062
r_ncsr_local_group_50.061
r_ncsr_local_group_210.06
r_ncsr_local_group_10.059
r_ncsr_local_group_70.059
r_ncsr_local_group_220.059
r_ncsr_local_group_270.059
r_ncsr_local_group_30.058
r_ncsr_local_group_130.057
r_ncsr_local_group_230.057
r_ncsr_local_group_350.057
r_ncsr_local_group_110.056
r_ncsr_local_group_180.056
r_ncsr_local_group_290.056
r_ncsr_local_group_310.056
r_ncsr_local_group_240.055
r_ncsr_local_group_320.055
r_ncsr_local_group_90.054
r_ncsr_local_group_100.054
r_ncsr_local_group_160.054
r_ncsr_local_group_200.053
r_ncsr_local_group_140.052
r_ncsr_local_group_340.052
r_ncsr_local_group_260.044
r_ncsr_local_group_40.042
r_ncsr_local_group_120.04
r_ncsr_local_group_190.036
r_ncsr_local_group_250.031
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms29178
Nucleic Acid Atoms
Solvent Atoms3122
Heterogen Atoms486

Software

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