Experiment: 5DBR

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4DJC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	298	0.2M sodium malonate pH 4.0, 20% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.086	α = 90
b = 58.086	β = 90
c = 102.638	γ = 120

Symmetry
Space Group	P 32 2 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	Bruker Platinum 135		2013-07-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.25	50.3	99.58	0.0905	18.4	15.6		9401

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)
	2.25	2.3	100		0.4455	4.1	10.56

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	4DJC	2.25	50.3	9401	543	99.58	0.2236	0.22	0.23	0.2842	0.28	RANDOM	39.957

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]
1.22	0.61		1.22		-3.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_4_deg	29.8
r_dihedral_angle_2_deg	27.785
r_dihedral_angle_3_deg	17.83
r_dihedral_angle_1_deg	6.42
r_mcangle_it	4.434
r_mcbond_it	3.35
r_mcbond_other	3.338
r_angle_refined_deg	1.913
r_angle_other_deg	1.101
r_chiral_restr	0.105

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_4_deg	29.8
r_dihedral_angle_2_deg	27.785
r_dihedral_angle_3_deg	17.83
r_dihedral_angle_1_deg	6.42
r_mcangle_it	4.434
r_mcbond_it	3.35
r_mcbond_other	3.338
r_angle_refined_deg	1.913
r_angle_other_deg	1.101
r_chiral_restr	0.105
r_bond_refined_d	0.018
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1196
Nucleic Acid Atoms
Solvent Atoms	12
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
PROTEUM PLUS	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.