X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.429824% w/v PEG 1500 20% v/v glycerol
Crystal Properties
Matthews coefficientSolvent content
2.4850.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.29α = 90
b = 102.71β = 90
c = 103.77γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2017-06-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97625DiamondI03

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
11.8143.2699.90.0570.0620.0240.9912.656.57872738.74
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)
11.811.8499.81.5231.650.630.721.16.7

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5mkr1.8137.4774723392399.820.193810.192170.22403RANDOM50.732
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]
-3.744.55-0.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.784
r_dihedral_angle_4_deg17.941
r_dihedral_angle_3_deg12.312
r_long_range_B_refined9.101
r_long_range_B_other9.093
r_scangle_other7.499
r_dihedral_angle_1_deg5.814
r_mcangle_it5.523
r_mcangle_other5.522
r_scbond_it5.118
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.784
r_dihedral_angle_4_deg17.941
r_dihedral_angle_3_deg12.312
r_long_range_B_refined9.101
r_long_range_B_other9.093
r_scangle_other7.499
r_dihedral_angle_1_deg5.814
r_mcangle_it5.523
r_mcangle_other5.522
r_scbond_it5.118
r_scbond_other5.117
r_mcbond_it4.123
r_mcbond_other4.123
r_angle_refined_deg1.491
r_angle_other_deg1.296
r_chiral_restr0.073
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms5829
Nucleic Acid Atoms
Solvent Atoms357
Heterogen Atoms112

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing