4GQP

Structure based design of sub-nanomolar affinity anti-methamphetamine single chain antibodies.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GKZPDB ENTRY 3GKZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.25287.150.917 M sodium citrate, pH 8.2, 0.324 M imidazole-malate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 287.15K
Crystal Properties
Matthews coefficientSolvent content
2.0239

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.516α = 90
b = 65.265β = 98.2
c = 48.483γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDRh coated flat mirrors2012-04-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.97946SSRLBL9-2

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
125099.20.08734.24.81429914299
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)
122.031000.338.15.1

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3GKZ238.661355471999.030.196690.193690.25361RANDOM27.454
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]
0.06-0.01-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.737
r_dihedral_angle_4_deg21.744
r_dihedral_angle_3_deg16.957
r_dihedral_angle_1_deg7.461
r_scangle_it4.36
r_scbond_it3.148
r_mcangle_it2.039
r_angle_refined_deg1.987
r_mcbond_it1.21
r_chiral_restr0.135
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.737
r_dihedral_angle_4_deg21.744
r_dihedral_angle_3_deg16.957
r_dihedral_angle_1_deg7.461
r_scangle_it4.36
r_scbond_it3.148
r_mcangle_it2.039
r_angle_refined_deg1.987
r_mcbond_it1.21
r_chiral_restr0.135
r_bond_refined_d0.023
r_gen_planes_refined0.01
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_mcangle_other
r_scbond_other
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 Atoms1756
Nucleic Acid Atoms
Solvent Atoms79
Heterogen Atoms11

Software

Software
Software NamePurpose
HKL-2000data collection
CCP4model building
REFMACrefinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing