X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5IQAPDB 5IQA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529680-120mM MgCl2, 8% glycerol, 10% PEG 3350, 100mM HEPES pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.8756.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.33α = 90
b = 99.78β = 105.43
c = 93.51γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002016-08-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.9795CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim 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
12.499.781000.1150.1420.0980.9926.13.86264240.53
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)
12.42.461001.0241.1980.7930.38313.7

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB 5IQA2.490.1459461315399.940.180260.177980.2233RANDOM57.621
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]
0.010.02-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.409
r_dihedral_angle_3_deg14.366
r_dihedral_angle_4_deg10.026
r_long_range_B_refined6.824
r_long_range_B_other6.824
r_dihedral_angle_1_deg6.244
r_angle_other_deg3.747
r_scangle_other3.092
r_mcangle_it2.415
r_mcangle_other2.415
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.409
r_dihedral_angle_3_deg14.366
r_dihedral_angle_4_deg10.026
r_long_range_B_refined6.824
r_long_range_B_other6.824
r_dihedral_angle_1_deg6.244
r_angle_other_deg3.747
r_scangle_other3.092
r_mcangle_it2.415
r_mcangle_other2.415
r_angle_refined_deg1.91
r_scbond_it1.908
r_scbond_other1.904
r_mcbond_it1.493
r_mcbond_other1.493
r_chiral_restr0.115
r_bond_refined_d0.018
r_gen_planes_other0.014
r_gen_planes_refined0.009
r_bond_other_d
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 Atoms9627
Nucleic Acid Atoms
Solvent Atoms716
Heterogen Atoms227

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
Cootmodel building