Experiment: 5U1A

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295	20% glycerol, 1.6 M NaCl, 8% PEG 6000, Hepes

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.412	α = 90
b = 128.412	β = 90
c = 165.041	γ = 90

Symmetry
Space Group	P 4

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	138	IMAGE PLATE	RIGAKU RAXIS IV++		2016-10-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	20	99.8	0.138	0.153	0.064	7.5	5.6		179122

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	2	2.03	100		0.895	0.991	0.423	0.69		5.4	8966

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	3bvf	2	20	170104	9002	99.72	0.1695	0.1681	0.1961	RANDOM	27.607

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]
0.22			0.22		-0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.111
r_dihedral_angle_4_deg	18.396
r_dihedral_angle_3_deg	14.604
r_dihedral_angle_1_deg	4.713
r_mcangle_it	3.291
r_mcbond_it	2.285
r_mcbond_other	2.282
r_angle_refined_deg	2.206
r_angle_other_deg	1.181
r_chiral_restr	0.148

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.111
r_dihedral_angle_4_deg	18.396
r_dihedral_angle_3_deg	14.604
r_dihedral_angle_1_deg	4.713
r_mcangle_it	3.291
r_mcbond_it	2.285
r_mcbond_other	2.282
r_angle_refined_deg	2.206
r_angle_other_deg	1.181
r_chiral_restr	0.148
r_bond_refined_d	0.026
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16422
Nucleic Acid Atoms
Solvent Atoms	1398
Heterogen Atoms	116

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
HKL	data scaling
HKL	data reduction

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.