X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52930.1 M Bicine-Tris, 12.5% PEG1000, 12.5% PEG3350, 12.5% MPD, 0.03 M calcium chloride, 0.03 M magnesium chloride
Crystal Properties
Matthews coefficientSolvent content
2.141.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.667α = 90
b = 80.916β = 96.07
c = 95.77γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2014-10-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.965ESRFMASSIF-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.547.6294.40.0649.22.6146071
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5985.20.6251.342.4

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 REPLACEMENTTHROUGHOUT3CHB1.547.62138740732994.450.223320.221410.25956RANDOM19.088
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]
-8.771.63-0.749.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.852
r_dihedral_angle_4_deg24.784
r_dihedral_angle_3_deg13.862
r_dihedral_angle_1_deg9.34
r_long_range_B_refined4.231
r_long_range_B_other4.231
r_scangle_other2.508
r_mcangle_it2.081
r_mcangle_other2.081
r_angle_refined_deg1.956
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.852
r_dihedral_angle_4_deg24.784
r_dihedral_angle_3_deg13.862
r_dihedral_angle_1_deg9.34
r_long_range_B_refined4.231
r_long_range_B_other4.231
r_scangle_other2.508
r_mcangle_it2.081
r_mcangle_other2.081
r_angle_refined_deg1.956
r_scbond_it1.653
r_scbond_other1.653
r_mcbond_it1.385
r_mcbond_other1.385
r_angle_other_deg1.181
r_chiral_restr0.151
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.003
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 Atoms8170
Nucleic Acid Atoms
Solvent Atoms654
Heterogen Atoms545

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing