X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HAW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP629330%(w/v) PEG3350, 0.5 M NaCl, 0.1 M glycine and 0.1 M citrate
Crystal Properties
Matthews coefficientSolvent content
2.448.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.53α = 107.397
b = 75.57β = 90.06
c = 85.67γ = 92.169
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16Mmirrors2018-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.00SPring-8BL41XU

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
12.24896.80.1230.1460.9926.883.4946190837.615
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)
12.22.3395.40.6370.7470.7641.983.665

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 REPLACEMENTTHROUGHOUT2HAW2.247.50960604298594.9730.2580.25610.297239.534
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]
-1.3141.854-0.1573.0410.448-1.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.751
r_dihedral_angle_4_deg16.04
r_dihedral_angle_3_deg14.76
r_dihedral_angle_1_deg7.124
r_lrange_it3.045
r_lrange_other3.025
r_mcangle_it1.631
r_mcangle_other1.631
r_scangle_it1.516
r_scangle_other1.516
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.751
r_dihedral_angle_4_deg16.04
r_dihedral_angle_3_deg14.76
r_dihedral_angle_1_deg7.124
r_lrange_it3.045
r_lrange_other3.025
r_mcangle_it1.631
r_mcangle_other1.631
r_scangle_it1.516
r_scangle_other1.516
r_angle_refined_deg1.4
r_angle_other_deg1.208
r_mcbond_it0.97
r_mcbond_other0.97
r_scbond_it0.894
r_scbond_other0.89
r_symmetry_nbd_refined0.341
r_nbd_refined0.189
r_nbd_other0.185
r_symmetry_nbd_other0.176
r_xyhbond_nbd_refined0.176
r_nbtor_refined0.152
r_symmetry_xyhbond_nbd_refined0.128
r_symmetry_xyhbond_nbd_other0.084
r_symmetry_nbtor_other0.075
r_xyhbond_nbd_other0.075
r_chiral_restr0.06
r_ncsr_local_group_10.039
r_ncsr_local_group_40.039
r_ncsr_local_group_20.038
r_ncsr_local_group_50.037
r_ncsr_local_group_60.033
r_ncsr_local_group_30.027
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_ext_dist_refined_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9360
Nucleic Acid Atoms
Solvent Atoms276
Heterogen Atoms10

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction