Experiment: 5DCQ

X-RAY DIFFRACTION

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.