X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
12980.1M Sodium Iodine 15% w/v PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3948.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.63α = 62.2
b = 68.41β = 68
c = 70.223γ = 71.58
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200IMAGE PLATERIGAKU2013-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT

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
12.8759.80175220602
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.872.9991.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3HBR2.8759.80122060209261134950.2040.2010.256RANDOM55.21
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]
0.88-0.730.140.58-0.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.219
r_dihedral_angle_3_deg19.655
r_dihedral_angle_4_deg18.163
r_dihedral_angle_1_deg6.947
r_mcangle_it4.144
r_mcbond_it2.526
r_mcbond_other2.525
r_scbond_it2.457
r_angle_refined_deg1.494
r_angle_other_deg1.258
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.219
r_dihedral_angle_3_deg19.655
r_dihedral_angle_4_deg18.163
r_dihedral_angle_1_deg6.947
r_mcangle_it4.144
r_mcbond_it2.526
r_mcbond_other2.525
r_scbond_it2.457
r_angle_refined_deg1.494
r_angle_other_deg1.258
r_chiral_restr0.077
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.006
r_gen_planes_other0.006
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7653
Nucleic Acid Atoms
Solvent Atoms69
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
HKL-2000data collection