X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ERBPDB entry 2ERB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52912 microliter drops, with equal volumes of protein at 50 mg/mL and reservoir solution containing 28% PEG 8000, 250 mM MgCl2, 50 mM Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
1.9236.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.248α = 90
b = 47.87β = 96.61
c = 69.082γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42006-04-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X12B0.9000NSLSX12B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.857099.60.07120.357.31907719077-321.43
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.9298.90.5474.47.38

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 REPLACEMENTTHROUGHOUTPDB entry 2ERB1.8568.68190771907797299.60.1540.1510.212RANDOM11.91
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]
-1.34-0.111.220.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.678
r_dihedral_angle_3_deg12.618
r_dihedral_angle_4_deg9.398
r_dihedral_angle_1_deg4.874
r_scangle_it3.114
r_scbond_it2.137
r_mcangle_it1.222
r_angle_refined_deg1.188
r_angle_other_deg0.824
r_mcbond_it0.733
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.678
r_dihedral_angle_3_deg12.618
r_dihedral_angle_4_deg9.398
r_dihedral_angle_1_deg4.874
r_scangle_it3.114
r_scbond_it2.137
r_mcangle_it1.222
r_angle_refined_deg1.188
r_angle_other_deg0.824
r_mcbond_it0.733
r_mcbond_other0.207
r_chiral_restr0.068
r_bond_refined_d0.01
r_gen_planes_refined0.005
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1935
Nucleic Acid Atoms
Solvent Atoms410
Heterogen Atoms59

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling