X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2980.1M sodium acetate trihydrate pH 4.0, 1,6M ammonium sulphate, 21mM ZnCl2
Crystal Properties
Matthews coefficientSolvent content
2.2645.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.4α = 90
b = 74.171β = 90
c = 116.82γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2014-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.885601ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.2562.6299.010.8077.994.123428
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.252.33199.444.2

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 REPLACEMENTTHROUGHOUT5NDL2.2562.6222150116099.070.194040.192060.23101RANDOM26.229
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]
-1.510.491.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.364
r_dihedral_angle_4_deg17.212
r_dihedral_angle_3_deg16.149
r_long_range_B_refined8.485
r_long_range_B_other8.464
r_dihedral_angle_1_deg7.605
r_scangle_other4.562
r_mcangle_it3.864
r_mcangle_other3.863
r_scbond_it2.813
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.364
r_dihedral_angle_4_deg17.212
r_dihedral_angle_3_deg16.149
r_long_range_B_refined8.485
r_long_range_B_other8.464
r_dihedral_angle_1_deg7.605
r_scangle_other4.562
r_mcangle_it3.864
r_mcangle_other3.863
r_scbond_it2.813
r_scbond_other2.812
r_mcbond_it2.313
r_mcbond_other2.31
r_angle_refined_deg1.616
r_angle_other_deg1.401
r_chiral_restr0.072
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms3664
Nucleic Acid Atoms
Solvent Atoms230
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing