1WPP | pdb_00001wpp

Structure of Streptococcus gordonii inorganic pyrophosphatase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP, STREAK SEEDING	5.6	293	sodium citrate, ammonium sulphate, K/Na-tartrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, STREAK SEEDING, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.3	47.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.08	α = 90
b = 148.96	β = 90
c = 43.72	γ = 90

Symmetry
Space Group	P 21 21 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	MARRESEARCH		2003-08-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7A	0.879	EMBL/DESY, HAMBURG	BW7A

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	2.05	20	97.8			40182	40182		-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	2.05	2.1	97.6

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	2.05	19.69	38171	38171	2010	100	0.16912	0.16912	0.16658	0.17	0.21647	0.22	RANDOM	22.56

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]
1.25			-1.35		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.889
r_scangle_it	4.093
r_scbond_it	2.544
r_angle_refined_deg	1.535
r_mcangle_it	1.494
r_mcbond_it	0.855
r_nbd_refined	0.18
r_symmetry_vdw_refined	0.18
r_symmetry_hbond_refined	0.157
r_xyhbond_nbd_refined	0.124
r_chiral_restr	0.111
r_metal_ion_refined	0.111
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
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_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4704
Nucleic Acid Atoms
Solvent Atoms	536
Heterogen Atoms	35

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data scaling
CNS	phasing