Experiment: 4DO4

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3H53	PDB entry 3H53

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	3.4	293	8-16% PEG3350, 70mM citric acid, 30mM Bis-Tris propane, pH 3.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.31	62.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 154.055	α = 90
b = 114.624	β = 95.82
c = 68.63	γ = 90

Symmetry
Space Group	C 1 2 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	CCD	ADSC QUANTUM 315	PT COATED MIRROR	2010-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.100	NSLS	X25

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.4	50	98.9	0.058	0.058	13.6	5.1		228468

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	1.4	1.42	94.9		0.842		4	10879

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	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 3H53	1.4	26.63	228268	11481	98.59	0.1433	0.1415	0.1776	RANDOM	31.11

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]
0.02		0.05	-0.05		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.79
r_dihedral_angle_4_deg	18.715
r_scangle_it	13.901
r_dihedral_angle_3_deg	12.647
r_scbond_it	10.819
r_mcangle_it	7.373
r_dihedral_angle_1_deg	6.186
r_mcbond_it	5.886
r_rigid_bond_restr	2.78
r_mcbond_other	2.365

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.79
r_dihedral_angle_4_deg	18.715
r_scangle_it	13.901
r_dihedral_angle_3_deg	12.647
r_scbond_it	10.819
r_mcangle_it	7.373
r_dihedral_angle_1_deg	6.186
r_mcbond_it	5.886
r_rigid_bond_restr	2.78
r_mcbond_other	2.365
r_angle_refined_deg	1.457
r_angle_other_deg	0.927
r_chiral_restr	0.085
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6279
Nucleic Acid Atoms
Solvent Atoms	991
Heterogen Atoms	363

Software

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