2B1H | pdb_00002b1h

Crystal structure analysis of anti-HIV-1 V3 Fab 2219 in complex with UG29 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	25% MPEG 5000, 0.2M disodium tartrate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.9	58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.899	α = 90
b = 94.501	β = 90
c = 96.617	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 4		2003-06-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	1.00	ALS	5.0.1

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	67.42	99.9	0.069	19.7	4.8	39609	39609		-3	33.6

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	2.03	100		0.612	2.6	4.8	1963

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 (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 2B0S	2	67.42	37576	37576	1982	99.78	0.20646	0.20646	0.20473	0.21	0.23837	0.24	RANDOM	35.055

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]
-1.19			2.5		-1.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.917
r_dihedral_angle_3_deg	15.336
r_dihedral_angle_4_deg	12.231
r_dihedral_angle_1_deg	7.348
r_scangle_it	3.235
r_scbond_it	2.38
r_angle_refined_deg	1.728
r_mcangle_it	1.495
r_mcbond_it	1.215
r_angle_other_deg	0.967
r_mcbond_other	0.27
r_symmetry_vdw_other	0.233
r_nbd_refined	0.218
r_nbd_other	0.198
r_symmetry_vdw_refined	0.186
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.163
r_chiral_restr	0.117
r_symmetry_hbond_refined	0.099
r_nbtor_other	0.088
r_bond_refined_d	0.02
r_gen_planes_refined	0.008
r_bond_other_d	0.004
r_gen_planes_other	0.001
r_xyhbond_nbd_other
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	3449
Nucleic Acid Atoms
Solvent Atoms	123
Heterogen Atoms

Software

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