1GC1

HIV-1 GP120 CORE COMPLEXED WITH CD4 AND A NEUTRALIZING HUMAN ANTIBODY


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HILPDB ENTRIES 1HIL, 1CDH AND 3CD4
experimental modelPDB 1CDHPDB ENTRIES 1HIL, 1CDH AND 3CD4
experimental modelPDB 3CD4PDB ENTRIES 1HIL, 1CDH AND 3CD4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7VAPOUR DIFFUSION CRYSTALLIZATION: 0.5 UL OF PROTEIN (~10MG/ML IN 350 MM NACL, 5 MM TRISCL PH 7.0) + 0.4 UL OF 0.1 M NACITRATE, 0.02 M NAHEPES, 10% ISOPROPANOL, 10.5% MONOMETHYL-PEG 5000, 0.0075% SEAPREP AGAROSE, PH 6.4 OVER A RESERVOIR OF 0.35 M NACL, 0.1 M NACITRATE, 0.02 M NAHEPES, 10% ISOPROPANOL, 10.5% MONOMETHYL-PEG 5000, PH 6.4, vapor diffusion
Crystal Properties
Matthews coefficientSolvent content
359

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.64α = 90
b = 88.13β = 90
c = 196.7γ = 90
Symmetry
Space GroupP 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEFUJIMIRRORS1996-08-09M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4ANSLSX4A

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
12.520860.0939.17337724-0.5
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)
12.52.5962.80.2472.171.56

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT + MULTIPLE ISOMORPHOUS REPLACEMENT + DENSITY MODIFICATIONTHROUGHOUTPDB ENTRIES 1HIL, 1CDH AND 3CD42.55228620143074.90.21030.21030.302RANDOM21
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]
RMS Deviations
KeyRefinement Restraint Deviation
x_scangle_it3.01
x_mcangle_it2.31
x_scbond_it1.97
x_angle_deg1.59
x_mcbond_it1.33
x_bond_d0.007
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
RMS Deviations
KeyRefinement Restraint Deviation
x_scangle_it3.01
x_mcangle_it2.31
x_scbond_it1.97
x_angle_deg1.59
x_mcbond_it1.33
x_bond_d0.007
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d
x_improper_angle_d_na
x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7080
Nucleic Acid Atoms
Solvent Atoms603
Heterogen Atoms194

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing