Experiment: 3SI1

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2AFM	PDB ENTRY 2AFM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.3	294	100 mM sodium acetate, 200 mM ammonium sulfate, 12% w/v PEG2000 MME, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.24	α = 90
b = 86.87	β = 90
c = 97.16	γ = 90

Symmetry
Space Group	P 21 21 21

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	MAR CCD 165 mm		2007-04-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1		BESSY	14.1

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	2.9	19.753	100	0.111	10.1	4.8	8528	8528	3		56.2

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	2.9	3	100		0.508	2.4	4.1

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 2AFM	2.9	19.753	8528	8527	426	99.49	0.2479	0.2479	0.2451	0.3006	RANDOM	48.3409

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]
2.96			-2.9		-0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.48
r_dihedral_angle_3_deg	25.714
r_dihedral_angle_4_deg	18.093
r_dihedral_angle_1_deg	11.331
r_scangle_it	2.729
r_angle_refined_deg	2.163
r_scbond_it	1.848
r_mcangle_it	1.373
r_mcbond_it	0.774
r_nbtor_refined	0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.48
r_dihedral_angle_3_deg	25.714
r_dihedral_angle_4_deg	18.093
r_dihedral_angle_1_deg	11.331
r_scangle_it	2.729
r_angle_refined_deg	2.163
r_scbond_it	1.848
r_mcangle_it	1.373
r_mcbond_it	0.774
r_nbtor_refined	0.34
r_nbd_refined	0.335
r_xyhbond_nbd_refined	0.292
r_symmetry_vdw_refined	0.285
r_chiral_restr	0.135
r_metal_ion_refined	0.044
r_bond_refined_d	0.019
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2631
Nucleic Acid Atoms
Solvent Atoms	52
Heterogen Atoms	29

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	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.