Experiment: 2P40

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
3.12	60.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.725	α = 90
b = 114.725	β = 90
c = 56.426	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				2004-05-13	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)	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	2.7	35	99.9	0.088	21.7	8.2	12041	12029			63.8

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	2.7	2.85	100		0.33	5.1	8.3	1750

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1L9K	2.701	31.27	11291	11291	720	100	0.20674	0.20674	0.20361	0.25468	RANDOM	46.159

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]
1.83	0.91		1.83		-2.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.242
r_dihedral_angle_3_deg	19.276
r_dihedral_angle_4_deg	14.618
r_dihedral_angle_1_deg	6.602
r_scangle_it	2.272
r_angle_refined_deg	1.433
r_scbond_it	1.285
r_mcangle_it	1.138
r_mcbond_it	0.641
r_nbtor_refined	0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.242
r_dihedral_angle_3_deg	19.276
r_dihedral_angle_4_deg	14.618
r_dihedral_angle_1_deg	6.602
r_scangle_it	2.272
r_angle_refined_deg	1.433
r_scbond_it	1.285
r_mcangle_it	1.138
r_mcbond_it	0.641
r_nbtor_refined	0.31
r_symmetry_vdw_refined	0.265
r_symmetry_hbond_refined	0.23
r_nbd_refined	0.21
r_xyhbond_nbd_refined	0.166
r_chiral_restr	0.1
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2061
Nucleic Acid Atoms
Solvent Atoms	42
Heterogen Atoms	107

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.