X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2931.92 M sodium malonate
Crystal Properties
Matthews coefficientSolvent content
2.2745.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 153.31α = 90
b = 66.75β = 106.54
c = 44.3γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-06-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97950DiamondI04

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
11.5742.4799.30.0540.0740.050.99811.33.359404
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)
11.571.6199.80.861.1650.7810.523.3

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 REPLACEMENTTHROUGHOUT3LDN1.5742.4756543286199.250.185420.184470.20411RANDOM25.081
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]
0.090.53-1.20.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.181
r_dihedral_angle_3_deg10.774
r_dihedral_angle_4_deg10.46
r_dihedral_angle_1_deg5.455
r_long_range_B_refined4.307
r_long_range_B_other4.092
r_scangle_other2.362
r_mcangle_it1.608
r_mcangle_other1.607
r_scbond_other1.439
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.181
r_dihedral_angle_3_deg10.774
r_dihedral_angle_4_deg10.46
r_dihedral_angle_1_deg5.455
r_long_range_B_refined4.307
r_long_range_B_other4.092
r_scangle_other2.362
r_mcangle_it1.608
r_mcangle_other1.607
r_scbond_other1.439
r_scbond_it1.438
r_angle_refined_deg1.225
r_mcbond_it0.977
r_mcbond_other0.977
r_angle_other_deg0.866
r_chiral_restr0.071
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.002
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 Atoms3231
Nucleic Acid Atoms
Solvent Atoms350
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing