Experiment: 4DKB

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4DK4	PDB ENTRY 4DK4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	290	20% w/v PEG3350, 0.2 M ammonium citrate tribasic, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.47	α = 90
b = 68.47	β = 90
c = 123.87	γ = 90

Symmetry
Space Group	P 43 21 2

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	ADSC QUANTUM 4		2010-06-12		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.976	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.831	48.416	100	0.11	0.11	18.5	13.7	26775	26775	1	1	20.1

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	1.831	1.93	100		0.584	0.584	1.3	13.1	3824

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 4DK4	1.831	48.416	26675	26675	1331	99.86	0.1702	0.1702	0.1688	0.1978	RANDOM	21.4041

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]
0.05			0.05		-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.899
r_scbond_it	28.336
r_scangle_it	24.393
r_dihedral_angle_3_deg	13.111
r_mcangle_it	12.524
r_mcbond_it	11.51
r_dihedral_angle_4_deg	10.979
r_dihedral_angle_1_deg	4.918
r_angle_refined_deg	1.44
r_angle_other_deg	0.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.899
r_scbond_it	28.336
r_scangle_it	24.393
r_dihedral_angle_3_deg	13.111
r_mcangle_it	12.524
r_mcbond_it	11.51
r_dihedral_angle_4_deg	10.979
r_dihedral_angle_1_deg	4.918
r_angle_refined_deg	1.44
r_angle_other_deg	0.95
r_mcbond_other	0.575
r_chiral_restr	0.093
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1761
Nucleic Acid Atoms
Solvent Atoms	135
Heterogen Atoms	26

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

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.