3V7M | pdb_00003v7m

Crystal structure of monoclonal human anti-Rhesus D Fc IgG1 T125(YB2/0) in the presence of Zn2+


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2J6E2J6E FC PORTION ONLY.

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.13168% MPEG 5000, 300 MICRO-M ZNCL2, 100 MICRO-M NICL2, 0.1 M SODIUM CACODYLATE, pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 316KK
Crystal Properties
Matthews coefficientSolvent content
2.9658.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.22α = 90
b = 147.75β = 90
c = 75.54γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4MIRRORS2003-06-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
12.024593.20.0630.05918.817.217681-247.34
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)
12.022.1470.10.7590.7122.716.62

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 REPLACEMENTTHROUGHOUT2J6E FC PORTION ONLY.2.0240.24167968841000.2370.2340.240.2860.29RANDOM47.93
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]
-1.13-0.451.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.152
r_dihedral_angle_3_deg22.107
r_dihedral_angle_4_deg20.147
r_dihedral_angle_1_deg7.136
r_scangle_it4.963
r_scbond_it3.185
r_mcangle_it2.576
r_angle_refined_deg2.136
r_mcbond_it1.465
r_chiral_restr0.154
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.152
r_dihedral_angle_3_deg22.107
r_dihedral_angle_4_deg20.147
r_dihedral_angle_1_deg7.136
r_scangle_it4.963
r_scbond_it3.185
r_mcangle_it2.576
r_angle_refined_deg2.136
r_mcbond_it1.465
r_chiral_restr0.154
r_bond_refined_d0.022
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1669
Nucleic Acid Atoms
Solvent Atoms142
Heterogen Atoms124

Software

Software
Software NamePurpose
DNAdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling