X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MLD 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529320% (w/v) PEG 10000, 0.1M HEPES pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.2445.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.218α = 90
b = 86.658β = 90
c = 135.05γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2018-02-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9SPring-8BL44XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)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
12.15099.90.0284074004327
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.141000.1865.76.8

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 REPLACEMENTTHROUGHOUT1MLD2.147.7537905201599.660.199110.195590.26591RANDOM40.391
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]
0.15-0.170.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.793
r_dihedral_angle_4_deg19.812
r_dihedral_angle_3_deg17.153
r_long_range_B_refined7.017
r_long_range_B_other7.017
r_dihedral_angle_1_deg6.676
r_scangle_other5.3
r_mcangle_other4.552
r_mcangle_it4.549
r_scbond_it3.554
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.793
r_dihedral_angle_4_deg19.812
r_dihedral_angle_3_deg17.153
r_long_range_B_refined7.017
r_long_range_B_other7.017
r_dihedral_angle_1_deg6.676
r_scangle_other5.3
r_mcangle_other4.552
r_mcangle_it4.549
r_scbond_it3.554
r_scbond_other3.554
r_mcbond_it3.208
r_mcbond_other3.201
r_angle_refined_deg1.91
r_angle_other_deg1.06
r_chiral_restr0.111
r_bond_refined_d0.016
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 Atoms5164
Nucleic Acid Atoms
Solvent Atoms157
Heterogen Atoms106

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing