Experiment: 3NOM

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2IWA	PDB ENTRY 2IWA

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.38	α = 90
b = 85.04	β = 108.16
c = 64.86	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		IMAGE PLATE	RIGAKU RAXIS IV++	confocal	2007-07-02	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	2.4	29	97.7	0.122	14.9			23164		-3	32.953

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.5	96.4		0.628	0.674	3.4

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 2IWA	2.4	28.98	23145	1158	100	0.2029	0.1994	0.2682	RANDOM	26.0348

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]
3.54		0.63	-1.93		-1.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.543
r_dihedral_angle_3_deg	18.194
r_dihedral_angle_4_deg	17.805
r_dihedral_angle_1_deg	8.05
r_scangle_it	4.069
r_scbond_it	2.595
r_angle_refined_deg	1.829
r_mcangle_it	1.697
r_mcbond_it	0.909
r_chiral_restr	0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.543
r_dihedral_angle_3_deg	18.194
r_dihedral_angle_4_deg	17.805
r_dihedral_angle_1_deg	8.05
r_scangle_it	4.069
r_scbond_it	2.595
r_angle_refined_deg	1.829
r_mcangle_it	1.697
r_mcbond_it	0.909
r_chiral_restr	0.11
r_bond_refined_d	0.02
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3794
Nucleic Acid Atoms
Solvent Atoms	109
Heterogen Atoms	18

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
XDS	data reduction

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.