3EJ0 | pdb_00003ej0

Crystal structure of inorganic pyrophosphatase from burkholderia pseudomallei with bound N-(pyridin-3-ylmethyl) aniline, H32 crystal form

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.4	289	100 MM IMIDAZOLE, PH 5.4, 20% PEG 3500, 100 MM SODIUM THIOCYANATE, 12.5 MM N-(pyridin-3-ylmethyl) aniline, pH 5.40, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.698	α = 90
b = 68.698	β = 90
c = 191.156	γ = 120

Symmetry
Space Group	H 3 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			2008-08-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.99987	ALS	5.0.1

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	1.96	50	99.8	0.076	10.6	5.1		12822

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	1.96	1.99	98.6		0.46		3.7

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.96	50	12820	624		0.201	0.198	0.2	0.252	0.25	RANDOM	33.16

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]
-0.06	-0.03		-0.06		0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.286
r_dihedral_angle_4_deg	15.38
r_dihedral_angle_3_deg	14.712
r_dihedral_angle_1_deg	5.313
r_scangle_it	3.433
r_scbond_it	2.131
r_mcangle_it	1.478
r_angle_refined_deg	1.394
r_mcbond_it	0.807
r_chiral_restr	0.095

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.286
r_dihedral_angle_4_deg	15.38
r_dihedral_angle_3_deg	14.712
r_dihedral_angle_1_deg	5.313
r_scangle_it	3.433
r_scbond_it	2.131
r_mcangle_it	1.478
r_angle_refined_deg	1.394
r_mcbond_it	0.807
r_chiral_restr	0.095
r_bond_refined_d	0.011
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1328
Nucleic Acid Atoms
Solvent Atoms	78
Heterogen Atoms	28

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
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.