3OAZ | pdb_00003oaz

A non-self sugar mimic of the HIV glycan shield shows enhanced antigenicity

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OP3	PDB entry 1OP3

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.623	α = 90
b = 72.092	β = 95.78
c = 84.074	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						M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B		APS	23-ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.75	29.65					85554

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 entry 1OP3	1.75	29.65	85506	4297	98.17	0.1782	0.1761	0.1905	0.2175	0.2315	RANDOM	23.494

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]
-1.4		-0.91	0.82		0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.669
r_dihedral_angle_4_deg	19.719
r_dihedral_angle_3_deg	13.927
r_dihedral_angle_1_deg	6.517
r_scangle_it	3.541
r_scbond_it	2.393
r_angle_refined_deg	1.508
r_mcangle_it	1.338
r_mcbond_it	0.745
r_chiral_restr	0.096
r_bond_refined_d	0.013
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6534
Nucleic Acid Atoms
Solvent Atoms	1003
Heterogen Atoms	116

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction