X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52980.005 M CoCl2, 0.005 M CdCl2, 0.005 M MgCl2, 0.005 M NiCl2, 0.1 M HEPES pH 7.5, 12% w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.6553.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.76α = 90
b = 75.47β = 90
c = 106.97γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002015-07-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-11.00CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.9643.6499.722.67.34280516.67

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 REPLACEMENTTHROUGHOUT3HBR1.9643.6440619212499.70.170.1680.21RANDOM25.4
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]
-1.21.21-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.418
r_dihedral_angle_4_deg20.202
r_dihedral_angle_3_deg12.944
r_long_range_B_refined5.918
r_dihedral_angle_1_deg5.873
r_long_range_B_other5.716
r_scangle_other4.546
r_scbond_it3.08
r_scbond_other3.079
r_mcangle_it2.586
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.418
r_dihedral_angle_4_deg20.202
r_dihedral_angle_3_deg12.944
r_long_range_B_refined5.918
r_dihedral_angle_1_deg5.873
r_long_range_B_other5.716
r_scangle_other4.546
r_scbond_it3.08
r_scbond_other3.079
r_mcangle_it2.586
r_mcangle_other2.586
r_mcbond_it1.95
r_mcbond_other1.949
r_angle_refined_deg1.78
r_angle_other_deg0.889
r_chiral_restr0.183
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.001
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 Atoms3942
Nucleic Acid Atoms
Solvent Atoms424
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing