Experiment: 5DQJ

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5DQD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	289.15	5% (w/v) glycerol and 15% (w/v) PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.607	α = 90
b = 139.872	β = 110.66
c = 72.076	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	Vertical focusing mirror	2011-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.9794	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.6	25	99.2	0.06	0.071	0.037	17	3.7		30002

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.69	100		0.619	0.721	0.367	0.823		3.8	3034

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5DQD	2.61	25	28504	1461	98.72	0.1949	0.1932	0.2	0.2281	0.23	RANDOM	67.347

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]
1.9		4.08	-2.57		-1.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.093
r_dihedral_angle_4_deg	22.103
r_dihedral_angle_3_deg	17.52
r_dihedral_angle_1_deg	6.646
r_mcangle_it	6.304
r_mcbond_it	4.086
r_mcbond_other	4.085
r_angle_refined_deg	1.356
r_angle_other_deg	0.954
r_chiral_restr	0.077

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.093
r_dihedral_angle_4_deg	22.103
r_dihedral_angle_3_deg	17.52
r_dihedral_angle_1_deg	6.646
r_mcangle_it	6.304
r_mcbond_it	4.086
r_mcbond_other	4.085
r_angle_refined_deg	1.356
r_angle_other_deg	0.954
r_chiral_restr	0.077
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.004
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6718
Nucleic Acid Atoms
Solvent Atoms	54
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

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.