3EIY | pdb_00003eiy

Crystal structure of inorganic pyrophosphatase from burkholderia pseudomallei with bound pyrophosphate

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.3	289	100 MM NA/K PHOSPHATE, PH 6.3, 49.5% PEG 200. CRYSTAL 3 MONTHS OLD., pH 6.30, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
3.81	67.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.952	α = 90
b = 100.952	β = 90
c = 111.233	γ = 120

Symmetry
Space Group	P 63 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	RIGAKU SATURN 944		2008-09-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	2.1	50	98.7	0.103	8.9	3.6		19792

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	2.1	2.18	98.5		0.669		2.7

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	2.1	50	19547	991		0.213	0.211	0.2117	0.249	0.2503	RANDOM	30.12

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]
0.8	0.4		0.8		-1.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.57
r_dihedral_angle_4_deg	18.89
r_dihedral_angle_3_deg	15.203
r_dihedral_angle_1_deg	5.857
r_scangle_it	3.551
r_scbond_it	2.198
r_mcangle_it	1.604
r_angle_refined_deg	1.46
r_mcbond_it	0.89
r_chiral_restr	0.092
r_bond_refined_d	0.015
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1330
Nucleic Acid Atoms
Solvent Atoms	112
Heterogen Atoms	39

Software

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