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, 9% PEG1000, 9% PEG3350, 9% MPD, 0.03 M calcium chloride, 0.03 M magnesium chloride
Crystal Properties
Matthews coefficientSolvent content
2.2244.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.543α = 90
b = 82.973β = 90
c = 196.555γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2014-07-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97625ESRFID29

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
11.649.1499.30.1266.64.7136523
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)
11.61.6998.91.0350.494.7

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 REPLACEMENTTHROUGHOUT3CHB1.649.14129701682299.190.184980.182810.22649RANDOM21.341
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]
-0.131.32-1.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.706
r_dihedral_angle_4_deg25.584
r_dihedral_angle_3_deg13.075
r_dihedral_angle_1_deg6.796
r_long_range_B_refined5.41
r_long_range_B_other5.41
r_scangle_other3.177
r_mcangle_other2.368
r_mcangle_it2.366
r_scbond_it2.044
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.706
r_dihedral_angle_4_deg25.584
r_dihedral_angle_3_deg13.075
r_dihedral_angle_1_deg6.796
r_long_range_B_refined5.41
r_long_range_B_other5.41
r_scangle_other3.177
r_mcangle_other2.368
r_mcangle_it2.366
r_scbond_it2.044
r_scbond_other2.042
r_angle_refined_deg1.809
r_mcbond_it1.552
r_mcbond_other1.546
r_angle_other_deg1.1
r_chiral_restr0.168
r_bond_refined_d0.014
r_gen_planes_refined0.008
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 Atoms950
Heterogen Atoms360

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing