2ZL6 | pdb_00002zl6

Atomic resolution structural characterization of recognition of histo-blood group antigens 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	3.8	293	0.1M Citric Acid(pH 3.8), 0.2M Ammonium Nitrate, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.512	α = 90
b = 83.512	β = 90
c = 162.929	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	1.43	41.73	99.7	0.07	8.9	5.38	121668	121303	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	1.43	1.48	99.1		0.532	2.5	5.4

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	1.43	40.45	115816	110616	5880	95.51	0.18023	0.17915	0.18	0.20048	0.2	RANDOM	18.633

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]
0.44	0.22		0.44		-0.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.146
r_dihedral_angle_4_deg	11.423
r_dihedral_angle_3_deg	10.891
r_dihedral_angle_1_deg	6.485
r_scangle_it	2.56
r_scbond_it	1.831
r_angle_refined_deg	1.391
r_mcangle_it	1.385
r_mcbond_it	0.813
r_nbtor_refined	0.312

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.146
r_dihedral_angle_4_deg	11.423
r_dihedral_angle_3_deg	10.891
r_dihedral_angle_1_deg	6.485
r_scangle_it	2.56
r_scbond_it	1.831
r_angle_refined_deg	1.391
r_mcangle_it	1.385
r_mcbond_it	0.813
r_nbtor_refined	0.312
r_nbd_refined	0.205
r_symmetry_hbond_refined	0.172
r_symmetry_vdw_refined	0.164
r_xyhbond_nbd_refined	0.146
r_chiral_restr	0.09
r_bond_refined_d	0.012
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4321
Nucleic Acid Atoms
Solvent Atoms	823
Heterogen Atoms	64

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.