3S36

Structural basis for the function of two anti-VEGF receptor antibodies


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52980.1 M imidazole, pH 6.5; 0.1 M CaCl2, 40% PEG 1500, 10% isopropanol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6653.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.864α = 90
b = 64.864β = 90
c = 263.161γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42009-08-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID1.0APS31-ID

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
13.25598.60.09920.810.21124011083-391.7
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)
13.23.3798.80.6883.210.51602

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3.254.96113241054852297.760.276980.274310.33187RANDOM124.403
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]
4.972.484.97-7.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.68
r_dihedral_angle_3_deg11.897
r_dihedral_angle_4_deg11.13
r_dihedral_angle_1_deg4.402
r_angle_refined_deg0.754
r_angle_other_deg0.686
r_scangle_it0.171
r_scbond_it0.095
r_mcangle_it0.071
r_chiral_restr0.046
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.68
r_dihedral_angle_3_deg11.897
r_dihedral_angle_4_deg11.13
r_dihedral_angle_1_deg4.402
r_angle_refined_deg0.754
r_angle_other_deg0.686
r_scangle_it0.171
r_scbond_it0.095
r_mcangle_it0.071
r_chiral_restr0.046
r_mcbond_it0.037
r_mcbond_other0.006
r_bond_refined_d0.004
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4104
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling