5NBW

Crystal structure of the Fab fragment 22F12 in complex with 3-hydroxybenzo[a]pyrene


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP52932.2 M Na-malonate
Crystal Properties
Matthews coefficientSolvent content
2.2846.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.15α = 90
b = 81β = 90
c = 186.16γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirrors2014-06-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.91841BESSY14.2

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
12.461.199.80.1199.44.635232
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)
12.42.5399.30.6042.64.8

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 REPLACEMENTTHROUGHOUT4M1G2.461.133462170499.660.182680.180350.22795RANDOM36.331
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]
-0.231.11-0.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.344
r_dihedral_angle_4_deg17.988
r_dihedral_angle_3_deg16.822
r_dihedral_angle_1_deg7.648
r_long_range_B_other6.004
r_long_range_B_refined5.902
r_mcangle_other3.857
r_mcangle_it3.856
r_scangle_other3.507
r_mcbond_it2.221
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.344
r_dihedral_angle_4_deg17.988
r_dihedral_angle_3_deg16.822
r_dihedral_angle_1_deg7.648
r_long_range_B_other6.004
r_long_range_B_refined5.902
r_mcangle_other3.857
r_mcangle_it3.856
r_scangle_other3.507
r_mcbond_it2.221
r_mcbond_other2.206
r_scbond_it2.071
r_scbond_other2.066
r_angle_refined_deg1.885
r_angle_other_deg1.055
r_chiral_restr0.106
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_bond_other_d0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6636
Nucleic Acid Atoms
Solvent Atoms242
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing