3V95 | pdb_00003v95

Crystal structure of monoclonal human anti-rhesus D Fc and IgG1 t125(yb2/0) in the presence of EDTA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3V8CPDB ENTRY 3V8C

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.129312.8% MPEG 5000, 21.5% ETHYLENE GLYCOL, 0.002M EDTA, 0.1 M SODIUM CACODYLATE, pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8356.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.38α = 90
b = 79.12β = 90
c = 138.91γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210MIRRORS2004-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.75099.40.090.117.567.815731-344.07
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.692.8597.20.5380.4913.787.8

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 3V8C2.741.8915731149437871000.2550.2510.250.3210.31RANDOM39.73
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]
-1.620.191.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.681
r_dihedral_angle_3_deg22.281
r_dihedral_angle_4_deg22.166
r_dihedral_angle_1_deg7.437
r_scangle_it2.653
r_angle_refined_deg1.795
r_scbond_it1.565
r_mcangle_it1.401
r_mcbond_it0.753
r_chiral_restr0.106
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.681
r_dihedral_angle_3_deg22.281
r_dihedral_angle_4_deg22.166
r_dihedral_angle_1_deg7.437
r_scangle_it2.653
r_angle_refined_deg1.795
r_scbond_it1.565
r_mcangle_it1.401
r_mcbond_it0.753
r_chiral_restr0.106
r_bond_refined_d0.013
r_gen_planes_refined0.008
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 Atoms3356
Nucleic Acid Atoms
Solvent Atoms108
Heterogen Atoms212

Software

Software
Software NamePurpose
DNAdata collection
REFMACrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing