Experiment: 3NDD

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6	295	0.1M MES/NaOH, 30% PEG 400, 35% glycerol, pH 6, VAPOR DIFFUSION, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.23	α = 90
b = 121.88	β = 113.88
c = 43.22	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 315		2009-07-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.97950	Diamond	I02

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	1.5	34.04	98.9	0.068	0.068	10.4	3.5	55516	55516			18.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.5	1.58	98.8		0.496	0.496	2.4	3.5	8057

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 1EZX	1.5	32.79	52634	2822	98.79	0.16235	0.15977	0.21118	RANDOM	21.412

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]
0.05		0.02	-0.04		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.773
r_dihedral_angle_4_deg	20.797
r_dihedral_angle_3_deg	13.445
r_sphericity_free	12.395
r_sphericity_bonded	7.175
r_scangle_it	6.925
r_dihedral_angle_1_deg	6.595
r_scbond_it	4.828
r_mcangle_it	3.487
r_rigid_bond_restr	2.806

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.773
r_dihedral_angle_4_deg	20.797
r_dihedral_angle_3_deg	13.445
r_sphericity_free	12.395
r_sphericity_bonded	7.175
r_scangle_it	6.925
r_dihedral_angle_1_deg	6.595
r_scbond_it	4.828
r_mcangle_it	3.487
r_rigid_bond_restr	2.806
r_mcbond_it	2.377
r_angle_refined_deg	2.083
r_chiral_restr	0.151
r_bond_refined_d	0.026
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2882
Nucleic Acid Atoms
Solvent Atoms	216
Heterogen Atoms

Software

Software
Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	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.