1F58 | pdb_00001f58

IGG1 FAB FRAGMENT (58.2) COMPLEX WITH 24-RESIDUE PEPTIDE (RESIDUES 308-333 OF HIV-1 GP120 (MN ISOLATE) WITH ALA TO AIB SUBSTITUTION AT POSITION 323


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ACYFAB 58.2 PORTION OF FAB 58.2/SER-LOOP PEPTIDE COMPLEX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.3pH 6.3
Crystal Properties
Matthews coefficientSolvent content
2.2746

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.89α = 90
b = 71.91β = 98.31
c = 88.25γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray295IMAGE PLATERIGAKU RAXIS IISUPER LONG MIRRORS (SIEMENS)1994-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU300

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
1243.699.60.10629.510.43046013.6
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)
22.0598.50.5473.4

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTFAB 58.2 PORTION OF FAB 58.2/SER-LOOP PEPTIDE COMPLEX24430460302499.60.1960.1960.190.2560.24RANDOM23.4
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_dihedral_angle_d28
x_scangle_it4.44
x_scbond_it3.17
x_mcangle_it2.81
x_angle_deg1.8
x_mcbond_it1.74
x_improper_angle_d1.57
x_bond_d0.01
x_bond_d_na
x_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d28
x_scangle_it4.44
x_scbond_it3.17
x_mcangle_it2.81
x_angle_deg1.8
x_mcbond_it1.74
x_improper_angle_d1.57
x_bond_d0.01
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_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3497
Nucleic Acid Atoms
Solvent Atoms120
Heterogen Atoms

Software

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