Experiment: 1NM9

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JXJ	pdb entry 1jxj

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	323	MPD, Calcium chloride, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 323K

Crystal Properties
Matthews coefficient	Solvent content
2.17	42.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.946	α = 90
b = 74.06	β = 90
c = 134.508	γ = 90

Symmetry
Space Group	P 21 21 21

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	mirrors	2002-09-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	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	2.1	42.6	99.7	0.069	19.1	6		31104			23.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.1	2.15	99.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1jxj	2.1	42.64	31104	29481	1564	99.47	0.1617	0.1617	0.16	0.19554	RANDOM	23.207

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]
-0.01			0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.112
r_scangle_it	2.228
r_scbond_it	1.401
r_angle_refined_deg	1.171
r_mcangle_it	0.985
r_mcbond_it	0.515
r_nbd_refined	0.196
r_symmetry_vdw_refined	0.191
r_symmetry_hbond_refined	0.135
r_xyhbond_nbd_refined	0.114

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.112
r_scangle_it	2.228
r_scbond_it	1.401
r_angle_refined_deg	1.171
r_mcangle_it	0.985
r_mcbond_it	0.515
r_nbd_refined	0.196
r_symmetry_vdw_refined	0.191
r_symmetry_hbond_refined	0.135
r_xyhbond_nbd_refined	0.114
r_chiral_restr	0.084
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3937
Nucleic Acid Atoms
Solvent Atoms	255
Heterogen Atoms	68

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	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.