Experiment: 5DCQ

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2XI9	2XI9, 3LTJ
experimental model	PDB	3LTJ	2XI9, 3LTJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277.15	magnesium formate, PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.688	α = 90
b = 113.688	β = 90
c = 152.623	γ = 120

Symmetry
Space Group	P 61

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	153	PIXEL	DECTRIS PILATUS 6M		2012-02-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.972	SOLEIL	PROXIMA 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	1.83	50	97.78	0.06	14.2	2.3		91861

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	1.83	1.94	97.7		0.642	1.9	2.3

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	2XI9, 3LTJ	1.83	50	96630	4769	97.78	0.1688	0.1671	0.2025	RANDOM	19.445

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]
0.21	0.1		0.21		-0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.56
r_dihedral_angle_3_deg	15.02
r_dihedral_angle_4_deg	14.041
r_dihedral_angle_1_deg	5.693
r_mcangle_it	2.946
r_mcbond_other	2.378
r_mcbond_it	2.377
r_angle_refined_deg	1.501
r_angle_other_deg	1.338
r_chiral_restr	0.091

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.56
r_dihedral_angle_3_deg	15.02
r_dihedral_angle_4_deg	14.041
r_dihedral_angle_1_deg	5.693
r_mcangle_it	2.946
r_mcbond_other	2.378
r_mcbond_it	2.377
r_angle_refined_deg	1.501
r_angle_other_deg	1.338
r_chiral_restr	0.091
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d	0.007
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8507
Nucleic Acid Atoms
Solvent Atoms	1102
Heterogen Atoms	36

Software

Software
Software Name	Purpose
XDS	data reduction
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XSCALE	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 R01GM133198.