Experiment: 1NAK

IGG1 FAB FRAGMENT (83.1) COMPLEX WITH 16-RESIDUE PEPTIDE (RESIDUES 304-321 OF HIV-1 GP120 (MN ISOLATE))

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ACY	PDB ENTRY 1ACY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	298	1.6M Na/K phosphate, 5% isopropanol, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.K

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.511	α = 90
b = 122.597	β = 108.54
c = 69.464	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	CUSTOM-MADE		2000-06-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	1.033	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.57	48.2	96.5	0.115	9.4	2.9	29751	29751		-3	42.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.57	2.66	80		0.394	2.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1ACY	2.57	48.08	29740	29740	1469	97.1	0.288	0.2898	0.326	0.3286	RANDOM	29.3

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]
6.69		2.24	-4.33		-2.36

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	26.9
c_angle_deg	1.6
c_improper_angle_d	0.98
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6770
Nucleic Acid Atoms
Solvent Atoms	107
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing
CNS	refinement