Experiment: 2P3O

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1L9K	PDB ENTRY 1L9K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.8	293	0.4 M Ammonium Sulfate, 0.1 M Sodium Citrate, 1.2 M Lithium Sulfate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.94	58.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.56	α = 90
b = 111.56	β = 90
c = 56.33	γ = 120

Symmetry
Space Group	P 31 2 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				2000-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.993	ESRF	ID14-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.756	27.96	97.1	0.083	27.4	5.2	10324	10025

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.756	2.95	97.1		0.515	3.4	5.1	1448

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1L9K	2.756	27.96	9592	9409	609	98.09	0.19783	0.19466	0.24372	RANDOM	65.565

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]
-2.2	-1.1		-2.2		3.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.239
r_dihedral_angle_4_deg	22.944
r_dihedral_angle_3_deg	18.451
r_dihedral_angle_1_deg	6.426
r_scangle_it	2.814
r_scbond_it	1.67
r_angle_refined_deg	1.615
r_mcangle_it	1.161
r_mcbond_it	0.685
r_nbtor_refined	0.306

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.239
r_dihedral_angle_4_deg	22.944
r_dihedral_angle_3_deg	18.451
r_dihedral_angle_1_deg	6.426
r_scangle_it	2.814
r_scbond_it	1.67
r_angle_refined_deg	1.615
r_mcangle_it	1.161
r_mcbond_it	0.685
r_nbtor_refined	0.306
r_symmetry_vdw_refined	0.281
r_nbd_refined	0.228
r_symmetry_hbond_refined	0.203
r_xyhbond_nbd_refined	0.143
r_chiral_restr	0.103
r_bond_refined_d	0.013
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2022
Nucleic Acid Atoms
Solvent Atoms	27
Heterogen Atoms	135

Software

Software
Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	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.