Experiment: 3I5N

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3CD8	PDB entry 3CD8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.8	298	15% PEG 4000, 0.1 M HEPES, 40 mM beta-mercaptoethanol, 6% isopropanol, 3% ethanol , pH 7.8, VAPOR DIFFUSION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.977	α = 90
b = 43.241	β = 90
c = 158.232	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	IMAGE PLATE	RIGAKU RAXIS IV++	varimax optics	2006-07-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	41.7	97.5	0.043	29.2	3.4	20349	19840			30.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2	2.07	93.3		0.174	7.1	2.8	1976

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	PDB entry 3CD8	2	41.7	19800	1007	97.77	0.227	0.225	0.21	0.267	0.26	RANDOM	32.707

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			2.06		-1.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.499
r_dihedral_angle_4_deg	18.571
r_dihedral_angle_3_deg	14.134
r_dihedral_angle_1_deg	4.964
r_scangle_it	1.315
r_mcangle_it	1.216
r_angle_refined_deg	1.025
r_scbond_it	0.892
r_mcbond_it	0.718
r_nbtor_refined	0.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.499
r_dihedral_angle_4_deg	18.571
r_dihedral_angle_3_deg	14.134
r_dihedral_angle_1_deg	4.964
r_scangle_it	1.315
r_mcangle_it	1.216
r_angle_refined_deg	1.025
r_scbond_it	0.892
r_mcbond_it	0.718
r_nbtor_refined	0.302
r_nbd_refined	0.171
r_symmetry_vdw_refined	0.127
r_xyhbond_nbd_refined	0.104
r_symmetry_hbond_refined	0.097
r_chiral_restr	0.069
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2244
Nucleic Acid Atoms
Solvent Atoms	206
Heterogen Atoms	29

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
DENZO	data reduction
AMoRE	phasing

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.