X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HIMPDB entry 2HIM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.1 M HEPES, 15% PEG 4000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1843.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.55α = 90
b = 123.31β = 92.35
c = 120.56γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2013-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-GAPS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.2120.4699.7146207
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.3498.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2HIM2.229.617145526138245728199.180.208490.206940.238RANDOM37.191
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]
0.44-0.180.41-0.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.902
r_dihedral_angle_4_deg19.817
r_dihedral_angle_3_deg12.983
r_long_range_B_refined7.94
r_long_range_B_other7.936
r_scangle_other5.836
r_dihedral_angle_1_deg5.823
r_mcangle_other4.892
r_mcangle_it4.571
r_scbond_other3.574
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.902
r_dihedral_angle_4_deg19.817
r_dihedral_angle_3_deg12.983
r_long_range_B_refined7.94
r_long_range_B_other7.936
r_scangle_other5.836
r_dihedral_angle_1_deg5.823
r_mcangle_other4.892
r_mcangle_it4.571
r_scbond_other3.574
r_scbond_it3.029
r_mcbond_it2.779
r_mcbond_other2.778
r_angle_refined_deg1.339
r_angle_other_deg1.065
r_chiral_restr0.072
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.006
r_gen_planes_other0.005
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 Atoms21650
Nucleic Acid Atoms
Solvent Atoms892
Heterogen Atoms120

Software

Software
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling