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
2.6353.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.08α = 90
b = 75.8β = 90
c = 106.67γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002014-07-15MSINGLE 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
11.7443.6299.930.67.461458

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 REPLACEMENTTHROUGHOUT3HBR1.7443.6258398298999.890.157650.156590.17837RANDOM25.564
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]
-1.141.090.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.736
r_dihedral_angle_4_deg21.546
r_dihedral_angle_3_deg13.065
r_long_range_B_refined6.91
r_long_range_B_other6.782
r_dihedral_angle_1_deg6.238
r_scangle_other5.722
r_scbond_it4.165
r_scbond_other4.165
r_mcangle_it3.177
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.736
r_dihedral_angle_4_deg21.546
r_dihedral_angle_3_deg13.065
r_long_range_B_refined6.91
r_long_range_B_other6.782
r_dihedral_angle_1_deg6.238
r_scangle_other5.722
r_scbond_it4.165
r_scbond_other4.165
r_mcangle_it3.177
r_mcangle_other3.161
r_mcbond_it2.654
r_mcbond_other2.654
r_angle_refined_deg1.558
r_angle_other_deg0.786
r_chiral_restr0.108
r_gen_planes_refined0.015
r_bond_refined_d0.012
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 Atoms3951
Nucleic Acid Atoms
Solvent Atoms459
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing