Experiment: 3E4D

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PV1	PDB code 1PV1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	PEG 3350, MgCl2, Bis-Tris buffer, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.433	α = 92.41
b = 68.949	β = 99.79
c = 95.648	γ = 98.47

Symmetry
Space Group	P 1

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		2006-03-01	M	SINGLE WAVELENGTH

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

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	2.01	32.4	95	0.058	23.2		106354	106354

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)
	2.02	2.09	80		0.288	4.3		106354

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB code 1PV1	2.01	25	106354	106327	5368	100	0.183	0.183	0.181	0.18	0.219	0.22	RANDOM	26.912

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]
0.39	1.32	-0.84	0.7	-0.15	-0.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.679
r_dihedral_angle_4_deg	11.911
r_dihedral_angle_3_deg	11.296
r_dihedral_angle_1_deg	5.423
r_scangle_it	2.216
r_scbond_it	1.456
r_angle_refined_deg	1.207
r_mcangle_it	0.927
r_mcbond_it	0.556
r_nbtor_refined	0.301

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.679
r_dihedral_angle_4_deg	11.911
r_dihedral_angle_3_deg	11.296
r_dihedral_angle_1_deg	5.423
r_scangle_it	2.216
r_scbond_it	1.456
r_angle_refined_deg	1.207
r_mcangle_it	0.927
r_mcbond_it	0.556
r_nbtor_refined	0.301
r_nbd_refined	0.184
r_symmetry_vdw_refined	0.173
r_symmetry_hbond_refined	0.124
r_xyhbond_nbd_refined	0.123
r_chiral_restr	0.089
r_metal_ion_refined	0.013
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13226
Nucleic Acid Atoms
Solvent Atoms	670
Heterogen Atoms	18

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
MrBUMP	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.