Experiment: 2R4U

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.7	277	40%(w/v) PEG 4000, 0.2 M Na tartrate and 0.1 M HEPPSO (pH 7.7), VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
5.7	78.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.166	α = 90
b = 126.166	β = 90
c = 151.745	γ = 90

Symmetry
Space Group	I 41

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	MARMOSAIC 225 mm CCD		2006-07-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 5ID-B	1.0	APS	5ID-B

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	2.367	97.66	98.1	0.059	11.9	5.1		47317		2.75	58.3

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)
	2.367	2.45	99		0.504	2.75	4.5	4785

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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	2QYY	2.367	97.13	2.75	47142	2386	97.66	0.21	0.183	0.182	0.203	RANDOM	41.926

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]
0.75			0.75		-1.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.478
r_dihedral_angle_4_deg	23.304
r_dihedral_angle_3_deg	18.106
r_dihedral_angle_1_deg	6.322
r_scangle_it	2.184
r_scbond_it	1.482
r_angle_refined_deg	1.448
r_mcangle_it	1.008
r_mcbond_it	0.567
r_nbtor_refined	0.307

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.478
r_dihedral_angle_4_deg	23.304
r_dihedral_angle_3_deg	18.106
r_dihedral_angle_1_deg	6.322
r_scangle_it	2.184
r_scbond_it	1.482
r_angle_refined_deg	1.448
r_mcangle_it	1.008
r_mcbond_it	0.567
r_nbtor_refined	0.307
r_symmetry_vdw_refined	0.218
r_nbd_refined	0.209
r_xyhbond_nbd_refined	0.144
r_symmetry_hbond_refined	0.125
r_chiral_restr	0.114
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3735
Nucleic Acid Atoms
Solvent Atoms	199
Heterogen Atoms	80

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

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.