8Z95 | pdb_00008z95

Humanized anti-PEG h6.3 Fab in complex with PEG


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6VL9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29318% (w/v) PEG-6000, 1% (w/v) PEG-2000-methyl ether, 0.15 M lithium sulfate monohydrate, and 0.1 M citric acid
Crystal Properties
Matthews coefficientSolvent content
2.8857.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 245.365α = 90
b = 43.574β = 111.7
c = 110.148γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2020-04-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B11NSRRCBL13B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
12.263099.10.05314.33.650690
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.272.3599.20.3330.3910.2020.93.7

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6VL92.2629.8148044261198.880.212140.209440.21740.261480.2649RANDOM38.145
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]
0.27-0.1-0.09-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.166
r_dihedral_angle_2_deg10.565
r_dihedral_angle_1_deg8.069
r_long_range_B_refined7.16
r_long_range_B_other7.158
r_scangle_other5.308
r_mcangle_it4.761
r_mcangle_other4.761
r_scbond_it3.426
r_scbond_other3.426
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.166
r_dihedral_angle_2_deg10.565
r_dihedral_angle_1_deg8.069
r_long_range_B_refined7.16
r_long_range_B_other7.158
r_scangle_other5.308
r_mcangle_it4.761
r_mcangle_other4.761
r_scbond_it3.426
r_scbond_other3.426
r_mcbond_it3.172
r_mcbond_other3.172
r_angle_refined_deg1.494
r_angle_other_deg0.532
r_chiral_restr0.064
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms6536
Nucleic Acid Atoms
Solvent Atoms180
Heterogen Atoms74

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
HKL-2000data collection
MOLREPphasing