Experiment: 5F1O

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YH3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	0.2M sodium acetate, 0.1M Tris-HCl, 25% PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.141	α = 90
b = 96.19	β = 90
c = 143.254	γ = 90

Symmetry
Space Group	P 21 21 21

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		2012-11-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.97852	SSRF	BL17U

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.2	50	99.2	0.074	13.4	7.6		24162

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	2.2	2.28	100		0.461		7.6	2353

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1YH3	2.2	50	22212	1200	96.35	0.1713	0.1679	0.2366	RANDOM	34.51

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]
0.06			0.94		-0.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.336
r_sphericity_free	28.62
r_dihedral_angle_4_deg	16.052
r_dihedral_angle_3_deg	13.67
r_dihedral_angle_1_deg	6.191
r_sphericity_bonded	4.49
r_mcangle_it	1.374
r_angle_refined_deg	1.305
r_mcbond_it	1.071
r_mcbond_other	1.071

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.336
r_sphericity_free	28.62
r_dihedral_angle_4_deg	16.052
r_dihedral_angle_3_deg	13.67
r_dihedral_angle_1_deg	6.191
r_sphericity_bonded	4.49
r_mcangle_it	1.374
r_angle_refined_deg	1.305
r_mcbond_it	1.071
r_mcbond_other	1.071
r_rigid_bond_restr	0.951
r_angle_other_deg	0.918
r_chiral_restr	0.081
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2958
Nucleic Acid Atoms
Solvent Atoms	207
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection

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.