Experiment: 4DDH

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	12% PEG3000, 150 mM Li2SO4, 0.1 M imidazole, 2% ethanol, 10% glycerol, 20 mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.58	α = 90
b = 70.93	β = 99.4
c = 82.01	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 225 mm CCD		2008-06-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.97	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.07	53.38	99.8	0.123	0.122	13.8	4.4	148474	33607		4

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	2.07	2.18	100		0.499	4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3COV	2.07	53.38	33657	31727	1693	99.34	0.19022	0.18705	0.19	0.24987	0.25	RANDOM	26.386

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]
0.82		-0.26	1.26		-2.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.74
r_dihedral_angle_4_deg	18.096
r_dihedral_angle_3_deg	16.724
r_dihedral_angle_1_deg	6.787
r_scangle_it	4.663
r_scbond_it	3.087
r_angle_refined_deg	1.996
r_mcangle_it	1.861
r_mcbond_it	1.113
r_chiral_restr	0.127

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.74
r_dihedral_angle_4_deg	18.096
r_dihedral_angle_3_deg	16.724
r_dihedral_angle_1_deg	6.787
r_scangle_it	4.663
r_scbond_it	3.087
r_angle_refined_deg	1.996
r_mcangle_it	1.861
r_mcbond_it	1.113
r_chiral_restr	0.127
r_bond_refined_d	0.024
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4174
Nucleic Acid Atoms
Solvent Atoms	430
Heterogen Atoms	75

Software

Software
Software Name	Purpose
DNA	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.