Experiment: 3K8B

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FAW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	298	phosphate buffer pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.999	α = 90
b = 79.515	β = 96.05
c = 64.385	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	IMAGE PLATE	MAR scanner 345 mm plate		2009-09-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.54

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	2.3	30	89.6	0.1096	3	2.47	58386	22860

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)
	2.3	2.38	94.7		0.3791	0.9	2.45

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1FAW	2.3	25.56	21698	1156	89.61	0.26676	0.26436	0.28	0.31146	0.32	RANDOM	47.187

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]
-0.09		0.04	0.06		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.607
r_dihedral_angle_3_deg	23.231
r_dihedral_angle_4_deg	21.662
r_dihedral_angle_1_deg	5.813
r_scbond_it	1.726
r_angle_refined_deg	1.525
r_mcangle_it	1.183
r_mcbond_it	0.701
r_symmetry_vdw_refined	0.352
r_metal_ion_refined	0.341

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.607
r_dihedral_angle_3_deg	23.231
r_dihedral_angle_4_deg	21.662
r_dihedral_angle_1_deg	5.813
r_scbond_it	1.726
r_angle_refined_deg	1.525
r_mcangle_it	1.183
r_mcbond_it	0.701
r_symmetry_vdw_refined	0.352
r_metal_ion_refined	0.341
r_nbtor_refined	0.315
r_symmetry_hbond_refined	0.304
r_nbd_refined	0.275
r_xyhbond_nbd_refined	0.208
r_chiral_restr	0.095
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4469
Nucleic Acid Atoms
Solvent Atoms	148
Heterogen Atoms	172

Software

Software
Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
AUTOMAR	data reduction
SCALEPACK	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.