Experiment: 2DUO

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1R1Z	PDB ENTRY 1R1Z

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	15% PEG4000, 1.5M NaCl, 0.1M MES (pH6.5), VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 170.7	α = 90
b = 45.4	β = 131.5
c = 116.1	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	CCD	ADSC QUANTUM 210		2005-10-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0000	Photon Factory	AR-NW12A

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	1.8	50	97.8	0.059	14.6	3.7	62420	61028			23.8

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)
	1.8	1.86	97.1		0.385	3.1	3.8	5986

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1R1Z	1.8	20	57775	57775	3080	97.8	0.206	0.206	0.205	0.21	0.241	0.24	RANDOM	25.14

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		1.74	0.03		1.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.585
r_dihedral_angle_3_deg	13.692
r_dihedral_angle_4_deg	10.133
r_dihedral_angle_1_deg	6.537
r_scangle_it	3.103
r_scbond_it	2.021
r_mcangle_it	1.413
r_angle_refined_deg	1.328
r_mcbond_it	0.884
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.585
r_dihedral_angle_3_deg	13.692
r_dihedral_angle_4_deg	10.133
r_dihedral_angle_1_deg	6.537
r_scangle_it	3.103
r_scbond_it	2.021
r_mcangle_it	1.413
r_angle_refined_deg	1.328
r_mcbond_it	0.884
r_nbtor_refined	0.304
r_symmetry_vdw_refined	0.197
r_nbd_refined	0.195
r_xyhbond_nbd_refined	0.136
r_symmetry_hbond_refined	0.102
r_chiral_restr	0.098
r_metal_ion_refined	0.059
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3957
Nucleic Acid Atoms
Solvent Atoms	421
Heterogen Atoms	13

Software

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