X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MDF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5289.150.2 M magnesium chloride hexahydrate, 0.1 M Tris hydrochloride pH 8.5 and 30 % (w/v) PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.0640

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.469α = 90
b = 40.802β = 115.57
c = 97.387γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80PIXELDECTRIS PILATUS 6M-FToroidal Mirror2018-07-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID291.07ESRFID29

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
11.945.2597.40.0530.0590.0330.99914.4324799
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)
11.95.166990.5730.690.3790.76123.1

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 REPLACEMENTTHROUGHOUT3MDF1.945.2523644120297.590.225430.22290.27606RANDOM33.978
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]
-0.8-0.82.35-0.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.246
r_dihedral_angle_4_deg22.166
r_dihedral_angle_3_deg16.802
r_long_range_B_refined7.512
r_long_range_B_other7.468
r_dihedral_angle_1_deg6.648
r_scangle_other5.473
r_mcangle_it4.651
r_mcangle_other4.651
r_scbond_it3.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.246
r_dihedral_angle_4_deg22.166
r_dihedral_angle_3_deg16.802
r_long_range_B_refined7.512
r_long_range_B_other7.468
r_dihedral_angle_1_deg6.648
r_scangle_other5.473
r_mcangle_it4.651
r_mcangle_other4.651
r_scbond_it3.54
r_scbond_other3.54
r_mcbond_it3.182
r_mcbond_other3.172
r_angle_refined_deg1.56
r_angle_other_deg1.365
r_chiral_restr0.075
r_bond_refined_d0.009
r_gen_planes_refined0.008
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 Atoms2467
Nucleic Acid Atoms
Solvent Atoms160
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
autoPROCdata scaling
MOLREPphasing