Experiment: 6VBH

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3Q8K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		288	Mixed 1:1 with 40% AmSO4, 200 mM Imidizole/Malate Buffer pH 4.2,100 mM MgCl2
2	VAPOR DIFFUSION, HANGING DROP		288	Mixed 1:1 wit 24% AmSO4, 200 mM Imidizole/Malate Buffer pH 4.2, 250 mM MgCl2, 0.5 mM SmSO4, 10 mM DTT
3	VAPOR DIFFUSION, HANGING DROP		288	Mixed 1:1 with 32% AmSO4, 10 mM DTT, 200 mM Imidizole/Malate Buffer pH 4.2, and 50 mM MgCl2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.438	α = 90
b = 173.403	β = 90
c = 101.608	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	ADSC QUANTUM 315		2010-07-08	M	SINGLE WAVELENGTH
2	2	x-ray	100	CCD	MARMOSAIC 325 mm CCD		2010-07-24	M	SINGLE WAVELENGTH
3	3	x-ray	100	CCD	MARMOSAIC 325 mm CCD		2010-07-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 12.3.1	1.115953	ALS	12.3.1
2	SYNCHROTRON	SSRL BEAMLINE BL11-1	1.1	SSRL	BL11-1
3	SYNCHROTRON	SSRL BEAMLINE BL11-1	1.1	SSRL	BL11-1

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	1.995	50	92.2	0.122	0.125	0.029	11.6	13.4		36003			42.97

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	2.03	66.5		0.725	0.797	0.319	0.814		4.5

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3q8k	1.995	43.833	32323	1602	82.55	0.2211	0.2198	0.2195	0.2444	0.2282	80.6006

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	9.051
f_angle_d	1.249
f_chiral_restr	0.062
f_bond_d	0.013
f_plane_restr	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2672
Nucleic Acid Atoms
Solvent Atoms	119
Heterogen Atoms	75

Software

Software
Software Name	Purpose
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	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.