1ZKE | pdb_00001zke

1.6 A Crystal Structure of a Protein HP1531 of Unknown Function from Helicobacter pylori

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	25% PEG3350, 0.1M NH4SO4, 0.1M Bis-Tris., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.6	52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.156	α = 90
b = 73.262	β = 90
c = 135.425	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	ADSC QUANTUM 315	mirrors	2004-12-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9797	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	1.6	50	92.5	0.067	24.48	4.5		75865	2	2	16.57

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	1.6	1.66	67.7		0.403	2.73	4	14527

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.6	67.73	72023	67687	3613	93.98	0.19996	0.19819	0.2	0.23181	0.24	RANDOM	16.567

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]
1.52			-0.89		-0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.455
r_dihedral_angle_4_deg	22.163
r_dihedral_angle_3_deg	14.067
r_scangle_it	4.289
r_dihedral_angle_1_deg	4.122
r_scbond_it	2.771
r_mcangle_it	1.325
r_angle_refined_deg	1.199
r_mcbond_it	0.777
r_nbtor_refined	0.306

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.455
r_dihedral_angle_4_deg	22.163
r_dihedral_angle_3_deg	14.067
r_scangle_it	4.289
r_dihedral_angle_1_deg	4.122
r_scbond_it	2.771
r_mcangle_it	1.325
r_angle_refined_deg	1.199
r_mcbond_it	0.777
r_nbtor_refined	0.306
r_metal_ion_refined	0.253
r_nbd_refined	0.201
r_symmetry_hbond_refined	0.174
r_symmetry_vdw_refined	0.153
r_xyhbond_nbd_refined	0.15
r_chiral_restr	0.074
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3930
Nucleic Acid Atoms
Solvent Atoms	753
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data scaling

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.