Experiment: 3BGK

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.9	289	0.49M sodium phosphate monobasic monohydrate, 0.91M Potassium phosphate dibasic, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
1.92	36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.527	α = 90
b = 96.527	β = 90
c = 56.26	γ = 90

Symmetry
Space Group	I 4

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV++	mirrors	2007-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	2.2909

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	2.5	25	94	0.053	0.053	29.5	10.86		8542			39.7

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)
	2.5	2.59	69.7		0.078	0.078	20.4	6.5	629

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	SAD	THROUGHOUT	2.5	20	10130	8521	413	93.98	0.21	0.208	0.2013	0.256	0.2459	RANDOM	20.225

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]
-0.99			-0.99		1.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.091
r_dihedral_angle_4_deg	17.484
r_dihedral_angle_3_deg	15.459
r_dihedral_angle_1_deg	5.103
r_scangle_it	1.614
r_angle_refined_deg	1.07
r_scbond_it	1.017
r_mcangle_it	0.78
r_mcbond_it	0.415
r_nbtor_refined	0.297

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.091
r_dihedral_angle_4_deg	17.484
r_dihedral_angle_3_deg	15.459
r_dihedral_angle_1_deg	5.103
r_scangle_it	1.614
r_angle_refined_deg	1.07
r_scbond_it	1.017
r_mcangle_it	0.78
r_mcbond_it	0.415
r_nbtor_refined	0.297
r_nbd_refined	0.196
r_symmetry_vdw_refined	0.174
r_xyhbond_nbd_refined	0.16
r_symmetry_hbond_refined	0.158
r_metal_ion_refined	0.112
r_chiral_restr	0.067
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2020
Nucleic Acid Atoms
Solvent Atoms	17
Heterogen Atoms	6

Software

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

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.