4HQX

CRYSTAL STRUCTURE OF HUMAN PDGF-BB IN COMPLEX WITH A Modified nucleotide aptamer (SOMAmer SL4)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MJGCHAIN A of 3MJG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.5289PROPLEX E1: 0.1 M MAGNESIUM ACETATE, 0.1 M SODIUM ACETATE PH 4.5, 8% PEG 8000, VAPOR DIFFUSION, TEMPERATURE 289K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
3.6866.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.43α = 90
b = 59.43β = 90
c = 168.16γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-08-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.979176APS19-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
12.319.67597.20.06419.2913750-350.08
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)
12.32.3698.40.5722.6

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 REPLACEMENTTHROUGHOUTCHAIN A of 3MJG2.319.675137506790.2410.2390.279RANDOM42.86
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]
2.332.33-4.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.582
r_dihedral_angle_4_deg25.856
r_dihedral_angle_3_deg14.965
r_dihedral_angle_1_deg6.101
r_angle_refined_deg2.005
r_chiral_restr0.1
r_bond_refined_d0.007
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms738
Nucleic Acid Atoms553
Solvent Atoms58
Heterogen Atoms2

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement