4KMT

Crystal structure of human germline antibody 5-51/O12


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9.52931.8 M ammonium sulfate, 0.1 M CHES, pH 9.5, 5% dioxane, cryoprotectant: 2.1 M ammonium sulfate, 0.1 M CHES, pH 9.5, 25% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5351.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.67α = 90
b = 73.83β = 90
c = 103.05γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDRIGAKU SATURN 944VARIMAX HF2009-05-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
12.13093.60.07916.84.92702627026-326
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)
12.12.1689.80.2785.73.5

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3QOT2.1152585725857109989.50.173160.173160.171160.21989RANDOM25.2
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]
0.01-0.20.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.958
r_scbond_it21.853
r_scangle_it21.825
r_dihedral_angle_4_deg12.478
r_dihedral_angle_3_deg12.184
r_dihedral_angle_1_deg5.886
r_mcangle_it3.605
r_mcbond_it2.008
r_angle_refined_deg1.021
r_chiral_restr0.062
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.958
r_scbond_it21.853
r_scangle_it21.825
r_dihedral_angle_4_deg12.478
r_dihedral_angle_3_deg12.184
r_dihedral_angle_1_deg5.886
r_mcangle_it3.605
r_mcbond_it2.008
r_angle_refined_deg1.021
r_chiral_restr0.062
r_bond_refined_d0.006
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3276
Nucleic Acid Atoms
Solvent Atoms302
Heterogen Atoms96

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling