Experiment: 3B0J

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3B0G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	277	PEG4000, Tris-HCl, MgCl2, MPD, pH 8.5, vapor diffusion, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.551	α = 90
b = 133.551	β = 90
c = 77.805	γ = 90

Symmetry
Space Group	P 4 21 2

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 210r	Rh-coated Si single crystal mirror	2009-10-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0	Photon Factory	AR-NW12A

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	1.7	50	98.4	0.078	0.078	38.28	11.9	76243	76423			23

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	1.7	1.76	93.7		0.431	7	10.4	7152

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3B0G	1.7	30.69	76059	72239	3820	100	0.1581	0.1581	0.1571	0.16	0.1762	0.17	RANDOM	16.7332

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]
-0.14			-0.14		0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.623
r_dihedral_angle_4_deg	12.959
r_dihedral_angle_3_deg	12.559
r_dihedral_angle_1_deg	5.966
r_scangle_it	3.301
r_scbond_it	1.996
r_angle_refined_deg	1.293
r_mcangle_it	1.129
r_mcbond_it	0.579
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.623
r_dihedral_angle_4_deg	12.959
r_dihedral_angle_3_deg	12.559
r_dihedral_angle_1_deg	5.966
r_scangle_it	3.301
r_scbond_it	1.996
r_angle_refined_deg	1.293
r_mcangle_it	1.129
r_mcbond_it	0.579
r_nbtor_refined	0.304
r_nbd_refined	0.208
r_symmetry_hbond_refined	0.203
r_symmetry_vdw_refined	0.171
r_xyhbond_nbd_refined	0.169
r_metal_ion_refined	0.133
r_chiral_restr	0.087
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4248
Nucleic Acid Atoms
Solvent Atoms	800
Heterogen Atoms	74

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	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 R01GM157729.