2YXF

The high resolution crystal structure of beta2-microglobulin under physiological conditions


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP728825% PEG 4000, 25% Glycerol, 0.06M ammoniumacetate, 0.1M MOPS, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties
Matthews coefficientSolvent content
2.1943.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.644α = 90
b = 28.907β = 121.59
c = 54.397γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDBruker DIP-60402005-12-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.65SPring-8BL44XU

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
11.1326.631000.05112.43.838852388529.459
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)
1.131.191000.33243.75630

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 2D4F1.1326.493885236904194899.980.184360.18380.19486RANDOM11.113
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]
-0.38-0.030.230.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.353
r_dihedral_angle_4_deg21.752
r_dihedral_angle_3_deg11.286
r_dihedral_angle_1_deg6.909
r_sphericity_free2.98
r_scangle_it2.541
r_rigid_bond_restr2.029
r_scbond_it1.978
r_sphericity_bonded1.845
r_mcangle_it1.369
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.353
r_dihedral_angle_4_deg21.752
r_dihedral_angle_3_deg11.286
r_dihedral_angle_1_deg6.909
r_sphericity_free2.98
r_scangle_it2.541
r_rigid_bond_restr2.029
r_scbond_it1.978
r_sphericity_bonded1.845
r_mcangle_it1.369
r_angle_refined_deg1.227
r_mcbond_it1.187
r_angle_other_deg0.744
r_mcbond_other0.302
r_symmetry_vdw_refined0.207
r_nbd_refined0.2
r_nbd_other0.195
r_nbtor_refined0.175
r_symmetry_hbond_refined0.15
r_symmetry_vdw_other0.142
r_xyhbond_nbd_refined0.139
r_nbtor_other0.084
r_chiral_restr0.08
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms828
Nucleic Acid Atoms
Solvent Atoms91
Heterogen Atoms

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling