Experiment: 3QDL

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	25 % PEG 3350, 0.1 M Bis-Tris, 0.2 M MgCl2, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.93	36.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.44	α = 90
b = 49.44	β = 90
c = 304.48	γ = 90

Symmetry
Space Group	P 41

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		2010-02-19	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MARMOSAIC 325 mm CCD		2010-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.8726	ESRF	ID23-2
2	SYNCHROTRON	ESRF BEAMLINE BM14	0.97625	ESRF	BM14

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	2	76.12	99.7	0.145	8.1	5.5	48813	48813

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	2	2.11	100		0.32	0.32	2.4	5.3	7115

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	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1icr	2	76.12	48807	2511	99.6	0.1898	0.1881	0.2203	RANDOM	19.935

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]
-0.36			-0.36		0.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.982
r_dihedral_angle_4_deg	16.34
r_dihedral_angle_3_deg	15.007
r_dihedral_angle_1_deg	4.915
r_scangle_it	0.933
r_angle_refined_deg	0.915
r_scbond_it	0.576
r_mcangle_it	0.509
r_mcbond_it	0.28
r_chiral_restr	0.061

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.982
r_dihedral_angle_4_deg	16.34
r_dihedral_angle_3_deg	15.007
r_dihedral_angle_1_deg	4.915
r_scangle_it	0.933
r_angle_refined_deg	0.915
r_scbond_it	0.576
r_mcangle_it	0.509
r_mcbond_it	0.28
r_chiral_restr	0.061
r_bond_refined_d	0.006
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5444
Nucleic Acid Atoms
Solvent Atoms	170
Heterogen Atoms	136

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.