X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1N8ZPDB entry 1N8Z

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.5292For crystallization of the Fab/VEGF (8-109) complex, equal volumes of protein complex solution (10.6 mg/ml protein, 300 mM NaCl, 25 mM Tris-HCl pH 7.5) and crystallization buffer containing 0.15 D, L Malic Acid pH 7.0, 20% PEG3350 were mixed and equilibrated at 19 C. Prior to data collection the crystals were cryo-protected by transfer between drops containing 5%, 10% and 15% Glycerol in artificial mother liquor, followed by flash freeze in liquid nitrogen, VAPOR DIFFUSION, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
3.1761.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.6α = 90
b = 197.978β = 90
c = 77.65γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-07-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21.00ALS5.0.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.65099.80.09166.22475524705
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.691000.65836.22419

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1N8Z2.63024225124899.810.1970.1940.252RANDOM40.479
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]
-1.01-0.561.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.833
r_dihedral_angle_4_deg15.435
r_dihedral_angle_3_deg15.219
r_dihedral_angle_1_deg6.122
r_scangle_it3.823
r_mcangle_it3.645
r_mcbond_it2.769
r_scbond_it2.67
r_angle_refined_deg1.255
r_angle_other_deg0.805
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.833
r_dihedral_angle_4_deg15.435
r_dihedral_angle_3_deg15.219
r_dihedral_angle_1_deg6.122
r_scangle_it3.823
r_mcangle_it3.645
r_mcbond_it2.769
r_scbond_it2.67
r_angle_refined_deg1.255
r_angle_other_deg0.805
r_mcbond_other0.517
r_symmetry_vdw_refined0.346
r_nbd_other0.19
r_nbd_refined0.185
r_nbtor_refined0.181
r_symmetry_vdw_other0.14
r_xyhbond_nbd_refined0.127
r_nbtor_other0.084
r_symmetry_hbond_refined0.075
r_chiral_restr0.072
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4072
Nucleic Acid Atoms
Solvent Atoms47
Heterogen Atoms6

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection