Experiment: 3LVW

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3IG5	PDB entry 3IG5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.8	291	100mM Hepes, pH 6.8, 14-20% PEG 400, 5mM GSH, 5mM MgCl2 , VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.62	66.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.127	α = 90
b = 118.127	β = 90
c = 165.799	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV++	Osmic Blue	2008-11-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.54

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	2.5	20	97.1	0.101	9.7	8.77		40046

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)
	2.5	2.59	96.1		0.533	3	8.9

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 3IG5	2.5	19.88	37458	2000	100	0.20171	0.1991	0.25054	RANDOM	46.214

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]
1.04			1.04		-2.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.511
r_dihedral_angle_4_deg	21.411
r_dihedral_angle_3_deg	17.139
r_dihedral_angle_1_deg	6.672
r_scangle_it	3.731
r_scbond_it	2.502
r_angle_refined_deg	1.926
r_mcangle_it	1.71
r_mcbond_it	1.025
r_nbtor_refined	0.322

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.511
r_dihedral_angle_4_deg	21.411
r_dihedral_angle_3_deg	17.139
r_dihedral_angle_1_deg	6.672
r_scangle_it	3.731
r_scbond_it	2.502
r_angle_refined_deg	1.926
r_mcangle_it	1.71
r_mcbond_it	1.025
r_nbtor_refined	0.322
r_nbd_refined	0.233
r_xyhbond_nbd_refined	0.158
r_symmetry_vdw_refined	0.147
r_chiral_restr	0.127
r_symmetry_hbond_refined	0.127
r_bond_refined_d	0.021
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5476
Nucleic Acid Atoms
Solvent Atoms	176
Heterogen Atoms	50

Software

Software
Software Name	Purpose
CrystalClear	data collection
PHENIX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

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.