Experiment: 3VY2

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	23% PEG 6000, 0.1M Tris, 0.2M sodium acetate, 19.8% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.868	α = 90
b = 83.038	β = 94.38
c = 40.239	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	95	CCD	ADSC QUANTUM 210r		2010-12-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.000	Photon Factory	BL-5A

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	1.6	20	99.5	0.045		7.4		31712

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	1.6	1.69	100		0.196		7.3

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1FLM	1.6	20	30085	1602	99.53	0.17146	0.17034	0.19202	RANDOM	18.68

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]
-0.58		-0.06	0.69		-0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.322
r_dihedral_angle_4_deg	16.16
r_dihedral_angle_3_deg	10.756
r_dihedral_angle_1_deg	5.563
r_scangle_it	2.805
r_scbond_it	1.684
r_mcangle_it	1.081
r_angle_refined_deg	1.058
r_mcbond_it	0.567
r_chiral_restr	0.075

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.322
r_dihedral_angle_4_deg	16.16
r_dihedral_angle_3_deg	10.756
r_dihedral_angle_1_deg	5.563
r_scangle_it	2.805
r_scbond_it	1.684
r_mcangle_it	1.081
r_angle_refined_deg	1.058
r_mcbond_it	0.567
r_chiral_restr	0.075
r_bond_refined_d	0.007
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1852
Nucleic Acid Atoms
Solvent Atoms	235
Heterogen Atoms	62

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

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.