Experiment: 4KM9

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4KM8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		281	20% PEG 3350, 0.2M Potassium chloride, vapor diffusion, hanging drop, temperature 281K

Crystal Properties
Matthews coefficient	Solvent content
2.41	49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.875	α = 90
b = 120.94	β = 90
c = 117.653	γ = 90

Symmetry
Space Group	C 2 2 21

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			2012-05-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	1.000	SSRF	BL17U

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	3.19	63.04	99.1	0.127	16.2	8.4		8956

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	3.2	3.31	100		0.492		8.6	864

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	4KM8	3.19	50	8939	426	98.76	0.2462	0.2434	0.24	0.3053	0.3	RANDOM	109.491

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]
0.13			3.58		-3.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.548
r_dihedral_angle_4_deg	19.054
r_dihedral_angle_3_deg	15.682
r_dihedral_angle_1_deg	4.92
r_mcangle_it	1.494
r_mcbond_it	1.008
r_angle_refined_deg	0.97
r_scangle_it	0.669
r_scbond_it	0.367
r_chiral_restr	0.064

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.548
r_dihedral_angle_4_deg	19.054
r_dihedral_angle_3_deg	15.682
r_dihedral_angle_1_deg	4.92
r_mcangle_it	1.494
r_mcbond_it	1.008
r_angle_refined_deg	0.97
r_scangle_it	0.669
r_scbond_it	0.367
r_chiral_restr	0.064
r_bond_refined_d	0.006
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2981
Nucleic Acid Atoms
Solvent Atoms	7
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.