2B1A

Crystal structure analysis of anti-HIV-1 V3 Fab 2219 in complex with UG1033 peptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2B0S	PDB ENTRY 2B0S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	13.75% PEG 20000, 0.05M disodium tartrate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.95	58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.716	α = 90
b = 96.89	β = 90
c = 97.018	γ = 90

Symmetry
Space Group	P 21 21 21

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 315		2003-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.98397	SSRL	BL11-1

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	2.348	31.31	98.6	0.057	31.9	3.7	24986	24986		-3	56

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	2.348	2.39	92.8		0.488	2.36	3.1	1118

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2B0S	2.348	31.31	23732	23732	1208	100	0.21287	0.21287	0.21118	0.24446	RANDOM	59.833

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]
-0.52			0.6		-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.416
r_dihedral_angle_4_deg	15.236
r_dihedral_angle_3_deg	14.904
r_dihedral_angle_1_deg	6.726
r_scangle_it	1.83
r_angle_refined_deg	1.328
r_scbond_it	1.222
r_angle_other_deg	0.849
r_mcangle_it	0.739
r_mcbond_it	0.628
r_symmetry_vdw_other	0.246
r_nbd_refined	0.199
r_nbd_other	0.197
r_symmetry_vdw_refined	0.185
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.13
r_xyhbond_nbd_other	0.11
r_mcbond_other	0.099
r_nbtor_other	0.085
r_chiral_restr	0.079
r_symmetry_hbond_refined	0.074
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3440
Nucleic Acid Atoms
Solvent Atoms	60
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
DENZO	data reduction