Experiment: 3D6I

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ERT	PDB Entry 1ERT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	290	0.1M MOPS, 20mM 2-ME, 68% ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.906	α = 90
b = 48.611	β = 116.76
c = 55.294	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	MARMOSAIC 300 mm CCD		2007-06-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID

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	1.5	50	95.9	0.062	18.7	3.5		35163	2

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)
	1.5	1.55	69.1		0.347		1.9	2534

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	PDB Entry 1ERT	1.5	49.39	35147	1752	95.74	0.225	0.223	0.249	RANDOM	18.605

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]
-0.17		-0.1	-0.08		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.35
r_dihedral_angle_3_deg	12.303
r_dihedral_angle_1_deg	5.077
r_scangle_it	4.002
r_scbond_it	2.735
r_mcangle_it	1.847
r_angle_refined_deg	1.302
r_mcbond_it	1.107
r_nbtor_refined	0.312
r_nbd_refined	0.208

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.35
r_dihedral_angle_3_deg	12.303
r_dihedral_angle_1_deg	5.077
r_scangle_it	4.002
r_scbond_it	2.735
r_mcangle_it	1.847
r_angle_refined_deg	1.302
r_mcbond_it	1.107
r_nbtor_refined	0.312
r_nbd_refined	0.208
r_symmetry_vdw_refined	0.183
r_xyhbond_nbd_refined	0.15
r_symmetry_hbond_refined	0.104
r_chiral_restr	0.078
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1721
Nucleic Acid Atoms
Solvent Atoms	145
Heterogen Atoms	10

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
HKL-2000	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.