Experiment: 4KSP

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	sitting drop, vapor diffusion	8.3	277	9.6 % PEG 8000, 0.8M LiCl, 100 mM Tris pH 8.3, sitting drop, vapor diffusion, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.5	64.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.495	α = 90
b = 111.495	β = 90
c = 145.487	γ = 90

Symmetry
Space Group	P 41 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	92	CCD	MARMOSAIC 300 mm CCD		2010-06-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1	APS	23-ID-B

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	2.93	50	99.8	0.157	5.4	6.7	20307	20267

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)
1	2.93	3	98.5		0.861		3.9	960

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4DBN	2.93	35	20307	20089	1031	98.4	0.1965	0.1941	0.2417	RANDOM	79.5058

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]
-0.89			-0.89		1.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.825
r_dihedral_angle_4_deg	18.188
r_dihedral_angle_3_deg	18.17
r_dihedral_angle_1_deg	5.896
r_angle_refined_deg	1.317
r_angle_other_deg	0.734
r_chiral_restr	0.066
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.825
r_dihedral_angle_4_deg	18.188
r_dihedral_angle_3_deg	18.17
r_dihedral_angle_1_deg	5.896
r_angle_refined_deg	1.317
r_angle_other_deg	0.734
r_chiral_restr	0.066
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4099
Nucleic Acid Atoms
Solvent Atoms	39
Heterogen Atoms	78

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction
MOLREP	phasing

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.