Experiment: 5JGY

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		291	15% (w/v) PEG 1500 and 0.1 M SPG buffer pH 4.5 added by 0.01 M of beta-NAD

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.75	α = 90
b = 115.301	β = 104.28
c = 56.466	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	100	CCD	ADSC QUANTUM 210		2009-07-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.9334	ESRF	ID14-1

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	1.45	57.65	98.6	0.048	11.37	1.9		230943		-3	21.264

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	1.45	1.54	98.6		0.644	1.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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		THROUGHOUT	1.45	57.65	112065	5866	99.87	0.1279	0.1261	0.1627	RANDOM	18.981

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]
0.42		0.02	-0.35		-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.653
r_sphericity_free	33.048
r_dihedral_angle_4_deg	16.601
r_dihedral_angle_3_deg	11.854
r_sphericity_bonded	10.926
r_dihedral_angle_1_deg	5.73
r_rigid_bond_restr	2.383
r_mcangle_it	2.127
r_mcbond_it	1.693
r_mcbond_other	1.692

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.653
r_sphericity_free	33.048
r_dihedral_angle_4_deg	16.601
r_dihedral_angle_3_deg	11.854
r_sphericity_bonded	10.926
r_dihedral_angle_1_deg	5.73
r_rigid_bond_restr	2.383
r_mcangle_it	2.127
r_mcbond_it	1.693
r_mcbond_other	1.692
r_angle_refined_deg	1.597
r_angle_other_deg	0.785
r_chiral_restr	0.076
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4874
Nucleic Acid Atoms
Solvent Atoms	713
Heterogen Atoms	228

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
BALBES	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 R01GM133198.