1WPN | pdb_00001wpn

Crystal structure of the N-terminal core of Bacillus subtilis inorganic pyrophosphatase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	hepes, ammonium sulphate, PEG-400, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.6	52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.14	α = 90
b = 60.97	β = 99.99
c = 74.06	γ = 90

Symmetry
Space Group	P 1 21 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 4		2004-02-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.933	ESRF	ID14-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.3	20	96			102851	102851		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.3	1.4	93.9

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 (All)	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	1.3	19.57	97706	97706	5143	100	0.14025	0.14025	0.13887	0.14	0.16648	0.17	RANDOM	15.914

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]
-0.46		-0.2	-0.6		0.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.702
r_scangle_it	5.082
r_sphericity_free	4.998
r_sphericity_bonded	4.482
r_scbond_it	3.34
r_mcangle_it	2.457
r_mcbond_it	1.683
r_angle_refined_deg	1.589
r_rigid_bond_restr	1.561
r_nbd_refined	0.191
r_symmetry_vdw_refined	0.19
r_symmetry_hbond_refined	0.124
r_xyhbond_nbd_refined	0.111
r_chiral_restr	0.108
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3062
Nucleic Acid Atoms
Solvent Atoms	512
Heterogen Atoms	19

Software

Software
Software Name	Purpose
REFMAC	refinement
ProDC	data collection
XDS	data scaling
MOLREP	phasing