3GHB | pdb_00003ghb

Crystal structure of anti-HIV-1 Fab 447-52D in complex with V3 peptide W2RW020

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Q1J	PDB ENTRY 1Q1J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	296.15	1.48M Ammonium Sulfate, 0.1M Tris pH 7.5, vapor diffusion, hanging drop, temperature 296.15K

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.273	α = 90
b = 76.214	β = 101.25
c = 113.915	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	ADSC QUANTUM 4	MIRRORS	2007-07-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A		NSLS	X4A

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.25	49.26	99.9	0.088	0.08		7.6		54517			25.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.25	2.33	99.4		0.485	0.485	4.6	7.3

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-Factor (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 1Q1J	2.25	49.26	56234	54128	2740	96.3	0.196	0.196	0.2	0.232	0.2	RANDOM	34.64

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]
-0.212		2.401	2.989		-2.777

RMS Deviations
Key	Refinement Restraint Deviation
c_angle_deg	1.37
c_bond_d	0.006
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d
c_improper_angle_d_na
c_improper_angle_d_prot
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6875
Nucleic Acid Atoms
Solvent Atoms	551
Heterogen Atoms	5

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing