Experiment: 1N8Y

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1M6B	PDB entry 1M6B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.4	298	15-30% PEG4000, 50mM Na citrate pH5.4, 10mM EDTA, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.18	61.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.87	α = 90
b = 116.4	β = 90
c = 55.37	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	ADSC QUANTUM 4		2001-02-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A		NSLS	X4A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	20	99.2		5.7	34177	33900	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.49	93.9		0.77	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	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 1M6B	2.4	20	1	1	34177	30022	1568	94.39	0.2266	0.2237	0.22375	0.28246	RANDOM	27.924

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]
1.25			-2.57		1.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.44
r_scangle_it	3.802
r_scbond_it	2.364
r_angle_refined_deg	1.724
r_mcangle_it	1.295
r_mcbond_it	0.675
r_symmetry_vdw_refined	0.274
r_nbd_refined	0.227
r_xyhbond_nbd_refined	0.16
r_symmetry_hbond_refined	0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.44
r_scangle_it	3.802
r_scbond_it	2.364
r_angle_refined_deg	1.724
r_mcangle_it	1.295
r_mcbond_it	0.675
r_symmetry_vdw_refined	0.274
r_nbd_refined	0.227
r_xyhbond_nbd_refined	0.16
r_symmetry_hbond_refined	0.14
r_chiral_restr	0.121
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4578
Nucleic Acid Atoms
Solvent Atoms	84
Heterogen Atoms	70

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement

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.