2ZL5 | pdb_00002zl5

Atomic resolution structural characterization of recognition of histo-blood group antigen by Norwalk virus

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1IHM	PDB ENTRY 1ihm

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.8	293	50mM Sodium acetate buffer(pH 4.8), 0.2M Ammonium Nitrate, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.517	α = 90
b = 83.517	β = 90
c = 163.368	γ = 120

Symmetry
Space Group	P 31 2 1

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 315		2007-08-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97942	APS	19-ID

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	1.47	41.76	99.1	0.066	10.1	5.99	112778	111763	2	2

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)
	1.47	1.52	98.1		0.498	2.7	6.03

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 (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 1ihm	1.47	33.1	107024	105740	5620	98.8	0.18178	0.18079	0.18	0.19992	0.2	RANDOM	17.901

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]
0.4	0.2		0.4		-0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.617
r_dihedral_angle_3_deg	10.893
r_dihedral_angle_4_deg	9.702
r_dihedral_angle_1_deg	6.433
r_scangle_it	2.732
r_scbond_it	1.951
r_mcangle_it	1.426
r_angle_refined_deg	1.386
r_mcbond_it	0.903
r_nbtor_refined	0.312

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.617
r_dihedral_angle_3_deg	10.893
r_dihedral_angle_4_deg	9.702
r_dihedral_angle_1_deg	6.433
r_scangle_it	2.732
r_scbond_it	1.951
r_mcangle_it	1.426
r_angle_refined_deg	1.386
r_mcbond_it	0.903
r_nbtor_refined	0.312
r_symmetry_hbond_refined	0.237
r_nbd_refined	0.208
r_symmetry_vdw_refined	0.163
r_xyhbond_nbd_refined	0.134
r_chiral_restr	0.091
r_bond_refined_d	0.012
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4354
Nucleic Acid Atoms
Solvent Atoms	677
Heterogen Atoms	16

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
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.