6CBU | pdb_00006cbu

Crystal structure of C4S3: A computationally designed immunogen to target Carbohydrate-Occluded Epitopes on the HIV envelope

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2W4C	2W4C Human common-type acylphosphatase variant, A99

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	30% PEG 3350, 200 mM Bis-tris, pH 6.5, 200 mM LiSO4

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 26.069	α = 90
b = 57.606	β = 90
c = 62.94	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	MARMOSAIC 225 mm CCD		2016-12-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.97817	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	1.2	50	98.4	0.056	0.059	0.016	18.9	14.1		30098

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.2	1.22	96.7		0.13	0.135	0.036	0.996		13.9

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	2W4C Human common-type acylphosphatase variant, A99	1.2	42.49	28610	1444	98.31	0.1435	0.143	0.14	0.1532	0.15	RANDOM	8.508

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.752
r_sphericity_free	16.344
r_dihedral_angle_4_deg	11.894
r_dihedral_angle_3_deg	10.509
r_dihedral_angle_1_deg	6.201
r_sphericity_bonded	3.712
r_rigid_bond_restr	1.84
r_angle_other_deg	1.693
r_angle_refined_deg	1.198
r_chiral_restr	0.082

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.752
r_sphericity_free	16.344
r_dihedral_angle_4_deg	11.894
r_dihedral_angle_3_deg	10.509
r_dihedral_angle_1_deg	6.201
r_sphericity_bonded	3.712
r_rigid_bond_restr	1.84
r_angle_other_deg	1.693
r_angle_refined_deg	1.198
r_chiral_restr	0.082
r_bond_refined_d	0.006
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	771
Nucleic Acid Atoms
Solvent Atoms	100
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

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.