4H0H | pdb_00004h0h

Crystal structure of mimicry-recognizing 2D10 scFv with peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4H0IPDB ENTRY 4H0I

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5277100 mM MES, pH 6.5, 1.6 M magnesium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4750.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.33α = 90
b = 80.33β = 90
c = 74.98γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATEMAR scanner 345 mm platemirrors2008-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

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
1269.5681000.06524.110.51931019310
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)
122.111000.4275.510.1

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4H0I225.51931017376189999.960.197250.195240.190.215250.22RANDOM30.55
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]
0.330.170.33-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.483
r_dihedral_angle_4_deg21.046
r_dihedral_angle_3_deg16.459
r_dihedral_angle_1_deg4.998
r_scangle_it4.546
r_scbond_it3.159
r_mcangle_it2.538
r_angle_refined_deg1.865
r_mcbond_it1.575
r_chiral_restr0.168
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.483
r_dihedral_angle_4_deg21.046
r_dihedral_angle_3_deg16.459
r_dihedral_angle_1_deg4.998
r_scangle_it4.546
r_scbond_it3.159
r_mcangle_it2.538
r_angle_refined_deg1.865
r_mcbond_it1.575
r_chiral_restr0.168
r_bond_refined_d0.028
r_gen_planes_refined0.015
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1914
Nucleic Acid Atoms
Solvent Atoms204
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
MAR345dtbdata collection