Experiment: 6BHE

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	291	25% PEG3350, 0.2 M sodium chloride, 0.1 M HEPES, 5% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.051	α = 90
b = 71.372	β = 104.23
c = 52.055	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	ADSC QUANTUM 315r		2013-07-10		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97856	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.33	41.2	99.8	0.049	0.057	0.03	0.999	15.3	3.7		60118

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.33	1.35	99.9		1.153	1.354	0.703	0.495		3.6	2964

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3DLM	1.35	35.69	54617	2872	99.76	0.1364	0.1345	0.15	0.1725	0.18	19.566

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]
-0.15		-0.29	-0.03		0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.815
r_sphericity_free	26.815
r_dihedral_angle_4_deg	17.422
r_sphericity_bonded	11.976
r_dihedral_angle_3_deg	11.549
r_dihedral_angle_1_deg	6.944
r_mcangle_it	2.887
r_mcbond_other	2.472
r_mcbond_it	2.469
r_rigid_bond_restr	2.153

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.815
r_sphericity_free	26.815
r_dihedral_angle_4_deg	17.422
r_sphericity_bonded	11.976
r_dihedral_angle_3_deg	11.549
r_dihedral_angle_1_deg	6.944
r_mcangle_it	2.887
r_mcbond_other	2.472
r_mcbond_it	2.469
r_rigid_bond_restr	2.153
r_angle_refined_deg	1.755
r_angle_other_deg	1.017
r_chiral_restr	0.114
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
r_bond_other_d	0.006
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1791
Nucleic Acid Atoms
Solvent Atoms	149
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	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.