3RU8 | pdb_00003ru8

Structure of an HIV epitope scaffold in complex with neutralizing antibody b12 Fab

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BOD	pdb entries 2BOD, 2NY7
experimental model	PDB	2NY7	pdb entries 2BOD, 2NY7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	18% PEG-3350, 0.22M potassium nitrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.453	α = 90
b = 93.097	β = 90
c = 94.373	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		CCD	ADSC QUANTUM 4		2010-07-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	1.0000	ALS	5.0.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.07	50	99.7	0.103	12.7	5.8		49114

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.07	2.11	95.3		0.34		5.2	2311

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (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 Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entries 2BOD, 2NY7	2.07	45.23	48971	2485	99.25	0.1696	0.1678	0.2	0.2026	0.22	RANDOM	40.2672

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]
0.06			-0.03		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.898
r_dihedral_angle_4_deg	20.392
r_dihedral_angle_3_deg	12.588
r_dihedral_angle_1_deg	5.906
r_scangle_it	3.12
r_scbond_it	2.021
r_mcangle_it	1.33
r_angle_refined_deg	1.166
r_angle_other_deg	0.805
r_mcbond_it	0.718

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.898
r_dihedral_angle_4_deg	20.392
r_dihedral_angle_3_deg	12.588
r_dihedral_angle_1_deg	5.906
r_scangle_it	3.12
r_scbond_it	2.021
r_mcangle_it	1.33
r_angle_refined_deg	1.166
r_angle_other_deg	0.805
r_mcbond_it	0.718
r_mcbond_other	0.17
r_chiral_restr	0.072
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5372
Nucleic Acid Atoms
Solvent Atoms	343
Heterogen Atoms	24

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.