Experiment: 3W43

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	298	10% PEG 1000, 0.1M Tris-HCl, 3mM MnCl2, pH 8.5, VAPOR DIFFUSION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.858	α = 90
b = 48.925	β = 93.61
c = 44.607	γ = 90

Symmetry
Space Group	P 1 21 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	RIGAKU JUPITER 210	Toroidal Mirror	2009-03-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.0000	SPring-8	BL38B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.22	50	96.8	0.035	33.6	3.6		50676		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.22	1.26	91.5		0.396	2.3	2.9

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3W45	1.22	15	50612	2586	96.87	0.1581	0.1565	0.1887	RANDOM	15.5347

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]
-0.43		0.34	0.46		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.88
r_dihedral_angle_3_deg	13.279
r_dihedral_angle_4_deg	13.25
r_dihedral_angle_1_deg	6.447
r_scangle_it	4.243
r_scbond_it	2.648
r_mcangle_it	2.065
r_angle_refined_deg	1.242
r_mcbond_it	1.17
r_rigid_bond_restr	1.094

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.88
r_dihedral_angle_3_deg	13.279
r_dihedral_angle_4_deg	13.25
r_dihedral_angle_1_deg	6.447
r_scangle_it	4.243
r_scbond_it	2.648
r_mcangle_it	2.065
r_angle_refined_deg	1.242
r_mcbond_it	1.17
r_rigid_bond_restr	1.094
r_chiral_restr	0.092
r_bond_refined_d	0.008
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1554
Nucleic Acid Atoms
Solvent Atoms	319
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
BSS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
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 R01GM133198.