Experiment: 3DAV

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		296.15	4.0 M sodium formate , VAPOR DIFFUSION, HANGING DROP, temperature 296.15K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.873	α = 90
b = 82.426	β = 92.59
c = 39.742	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	273	IMAGE PLATE	MAR scanner 345 mm plate		2008-03-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	OTHER	1.54

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	2.2	50	95.8	0.09	0.069	15.28	2.9		11429

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)
	2.2	2.27	64		0.318	0.343	4.03	2.2	747

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		THROUGHOUT	3D9Y	2.2	41.2	10814	11348	534	96.55	0.176	0.176	0.174	0.26	RANDOM	24.058

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		-0.11	-0.45		0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.433
r_dihedral_angle_3_deg	16.339
r_dihedral_angle_4_deg	14.637
r_dihedral_angle_1_deg	5.317
r_scangle_it	1.5
r_angle_refined_deg	1.146
r_scbond_it	0.903
r_mcangle_it	0.561
r_symmetry_metal_ion_refined	0.467
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.433
r_dihedral_angle_3_deg	16.339
r_dihedral_angle_4_deg	14.637
r_dihedral_angle_1_deg	5.317
r_scangle_it	1.5
r_angle_refined_deg	1.146
r_scbond_it	0.903
r_mcangle_it	0.561
r_symmetry_metal_ion_refined	0.467
r_nbtor_refined	0.304
r_mcbond_it	0.299
r_symmetry_vdw_refined	0.204
r_nbd_refined	0.194
r_xyhbond_nbd_refined	0.148
r_symmetry_hbond_refined	0.125
r_chiral_restr	0.088
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1868
Nucleic Acid Atoms
Solvent Atoms	231
Heterogen Atoms	9

Software

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