Experiment: 5BYN

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	Hepes-Na, ammonium sulfate, PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 190.64	α = 90
b = 190.64	β = 90
c = 190.64	γ = 90

Symmetry
Space Group	F 2 3

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	MAR CCD 165 mm		2012-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	1.42	LNLS	W01B-MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	2.651	110.066	99.9	0.117	0.126	0.048	9.8	6.6	16760	16760

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.65	2.79	99.9		0.336	0.336	0.153	2	5.6	2431

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.651	38.91	15900	858	99.82	0.2075	0.2039	0.2779	RANDOM	42.582

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]
-7.75	18.28	-4.62	21.51	-7.69	-13.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.2
r_dihedral_angle_4_deg	20.434
r_dihedral_angle_3_deg	17.887
r_dihedral_angle_1_deg	7.79
r_sphericity_free	7.031
r_sphericity_bonded	2.462
r_rigid_bond_restr	2.453
r_angle_other_deg	2.294
r_angle_refined_deg	1.827
r_mcangle_it	1.564

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.2
r_dihedral_angle_4_deg	20.434
r_dihedral_angle_3_deg	17.887
r_dihedral_angle_1_deg	7.79
r_sphericity_free	7.031
r_sphericity_bonded	2.462
r_rigid_bond_restr	2.453
r_angle_other_deg	2.294
r_angle_refined_deg	1.827
r_mcangle_it	1.564
r_mcbond_it	1.175
r_mcbond_other	1.175
r_chiral_restr	0.093
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3589
Nucleic Acid Atoms
Solvent Atoms	65
Heterogen Atoms	68

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
MOLREP	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.