Experiment: 6HBE

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3X1E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	0.2 M CaCl2.2H2O, 0.1 M HEPES sodium pH: 7.5, 28% w/v PEG 400

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 145.692	α = 90
b = 110.553	β = 107.51
c = 88.81	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	PIXEL	DECTRIS PILATUS 6M		2017-01-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.928190	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.63	86.51	98.4	0.049	0.049	0.059	0.032	0.998	11.8	3.4		163764

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	1.63	1.72	100		0.454	0.543	0.295	0.888		3.3

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	3X1E	1.63	86.51	155447	8316	98.35	0.1627	0.1612	0.17	0.1901	0.2	RANDOM	29.474

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]
3.73		-1.26	-1.7		-1.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.02
r_dihedral_angle_4_deg	16.869
r_dihedral_angle_3_deg	12.151
r_dihedral_angle_1_deg	7.27
r_angle_refined_deg	1.488
r_angle_other_deg	0.935
r_chiral_restr	0.096
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.02
r_dihedral_angle_4_deg	16.869
r_dihedral_angle_3_deg	12.151
r_dihedral_angle_1_deg	7.27
r_angle_refined_deg	1.488
r_angle_other_deg	0.935
r_chiral_restr	0.096
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9978
Nucleic Acid Atoms
Solvent Atoms	853
Heterogen Atoms	12

Software

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

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.