X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RZKYU2core/CD4 d1d2 from PDB entry 1RZK and 412d Fab from PDB entry 1RZG
experimental modelPDB 412DYU2core/CD4 d1d2 from PDB entry 1RZK and 412d Fab from PDB entry 1RZG
experimental modelPDB 1RZGYU2core/CD4 d1d2 from PDB entry 1RZK and 412d Fab from PDB entry 1RZG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529317-19% polyethylene glycol (PEG) 1500, 0.1 M Na cacodylate pH 6.5, 0.2 M Na malonate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.0259.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.6α = 90
b = 53.021β = 104.64
c = 225.326γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2004-04-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.00APS22-ID

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
13.35067.80.1330.1339.13.125816-3
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)
13.33.4216.20.5371.31.7595

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTYU2core/CD4 d1d2 from PDB entry 1RZK and 412d Fab from PDB entry 1RZG3.3203840125600132966.70.2020.269random156
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]
-46.386-20.02116.9129.475
RMS Deviations
KeyRefinement Restraint Deviation
f_angle_deg1.092
f_bond_d0.0054
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14497
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms490

Software

Software
Software NamePurpose
PHENIXrefinement
AMoREphasing
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling