X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52930.1 M Bis Tris propane pH 8.5, 0.2M Sodium nitrate, 20% w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.3748.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46α = 90
b = 91.78β = 112.11
c = 53.52γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray173PIXELDECTRIS PILATUS3 6M2015-02-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97625ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.945.8994.40.0650.99710.033.230909
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.95660.7270.5672.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5MWR1.945.8929363154694.590.188550.186360.23038RANDOM39.364
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]
-2.21-1.094.05-0.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.624
r_dihedral_angle_4_deg22.726
r_dihedral_angle_3_deg14.545
r_long_range_B_refined8.772
r_long_range_B_other8.766
r_scangle_other7.171
r_dihedral_angle_1_deg5.786
r_scbond_it4.727
r_scbond_other4.726
r_mcangle_it4.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.624
r_dihedral_angle_4_deg22.726
r_dihedral_angle_3_deg14.545
r_long_range_B_refined8.772
r_long_range_B_other8.766
r_scangle_other7.171
r_dihedral_angle_1_deg5.786
r_scbond_it4.727
r_scbond_other4.726
r_mcangle_it4.303
r_mcangle_other4.302
r_mcbond_other3.188
r_mcbond_it3.187
r_angle_refined_deg2.021
r_angle_other_deg1.031
r_chiral_restr0.236
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms3054
Nucleic Acid Atoms
Solvent Atoms67
Heterogen Atoms122

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
XSCALEdata scaling
PHASERphasing
XDSdata reduction