3T43 | pdb_00003t43

Crystal Structure of HIV Epitope-Scaffold 4E10_1XIZA_S0_006_C

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3LF6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	10% PEG 4000, 20% Isopropanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.32	47.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.06	α = 90
b = 65.27	β = 99.57
c = 73.1	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	298	IMAGE PLATE	RIGAKU RAXIS IV++		2007-04-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.95	30.31	99.7	0.052	0.052	12.5	3.04		24452

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	1.95	2.02	99.6		0.273	2	1.84	2431

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	3LF6	1.95	30.31	23184	1249	99.66	0.2063	0.204	0.21	0.2492	0.25	RANDOM	44.3047

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]
0.02		-0.02	0.01		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.994
r_dihedral_angle_4_deg	19.399
r_dihedral_angle_3_deg	12.06
r_dihedral_angle_1_deg	4.711
r_scangle_it	2.94
r_scbond_it	1.987
r_mcangle_it	1.535
r_angle_refined_deg	1.04
r_mcbond_it	0.936
r_angle_other_deg	0.775
r_symmetry_vdw_other	0.377
r_symmetry_hbond_refined	0.207
r_nbd_refined	0.204
r_nbd_other	0.201
r_mcbond_other	0.196
r_xyhbond_nbd_refined	0.19
r_nbtor_refined	0.181
r_nbtor_other	0.088
r_symmetry_vdw_refined	0.087
r_chiral_restr	0.062
r_bond_refined_d	0.009
r_xyhbond_nbd_other	0.006
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2394
Nucleic Acid Atoms
Solvent Atoms	194
Heterogen Atoms

Software

Software
Software Name	Purpose
d*TREK	data scaling
d*TREK	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
PHASER	phasing