4U12 | pdb_00004u12

Crystal structure of protein HP0242 from Helicobacter pylori at 1.94 A resolution: a knotted homodimer

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	293	30% v/v Pentaerythritol Ethoxylate (15/4 EO/OH), 0.05M Ammonium Sulfate, 0.05M Bis-Tris, pH 6.5,

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.944	α = 90
b = 44.944	β = 90
c = 117.883	γ = 90

Symmetry
Space Group	P 43 2 2

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	SBC-3	Mirrors	2006-06-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97904	APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.94	50	99.8	0.06	0.06	8.7	16		9566			36.3

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	1.94	1.97	100		0.937		16.7	465

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.94	44.94	9526	457	99.79	0.2224	0.2208	0.23	0.2533	0.26	RANDOM	65.103

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]
0.17			0.17		-0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.838
r_dihedral_angle_3_deg	16.75
r_dihedral_angle_4_deg	5.492
r_dihedral_angle_1_deg	4.217
r_mcangle_it	2.261
r_mcbond_it	1.601
r_mcbond_other	1.585
r_angle_refined_deg	1.411
r_angle_other_deg	0.804
r_chiral_restr	0.082

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.838
r_dihedral_angle_3_deg	16.75
r_dihedral_angle_4_deg	5.492
r_dihedral_angle_1_deg	4.217
r_mcangle_it	2.261
r_mcbond_it	1.601
r_mcbond_other	1.585
r_angle_refined_deg	1.411
r_angle_other_deg	0.804
r_chiral_restr	0.082
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	626
Nucleic Acid Atoms
Solvent Atoms	69
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SCALEPACK	data scaling
HKL-3000	phasing
SHELXDE	phasing
DM	phasing
RESOLVE	phasing
ARP	model building
Coot	model building
PDB_EXTRACT	data extraction
REFMAC	refinement

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.