Experiment: 3D1J

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	40% (w/v) PEG 4000, 0.1 M Tris, 0.2 M Na tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4.23	70.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 232.959	α = 90
b = 232.959	β = 90
c = 85.539	γ = 120

Symmetry
Space Group	H 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	98	CCD	MAR CCD 165 mm		2004-10-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 32-ID	1.0	APS	32-ID

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	3	50	99.2	0.076	28.3	9.4	21907	20539		2	63.9

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)
	3	3.15	100		0.345	2	9.6	2180

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	PDB ENTRY 1RZU	3	50	2	17683	879	99.08	0.249	0.212	0.209	0.263	RANDOM	50.651

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]
1.29	0.64		1.29		-1.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.309
r_dihedral_angle_4_deg	20.682
r_dihedral_angle_3_deg	19.349
r_dihedral_angle_1_deg	6.225
r_mcangle_it	1.546
r_angle_refined_deg	1.469
r_scangle_it	1.076
r_mcbond_it	0.882
r_scbond_it	0.681
r_nbtor_refined	0.346

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.309
r_dihedral_angle_4_deg	20.682
r_dihedral_angle_3_deg	19.349
r_dihedral_angle_1_deg	6.225
r_mcangle_it	1.546
r_angle_refined_deg	1.469
r_scangle_it	1.076
r_mcbond_it	0.882
r_scbond_it	0.681
r_nbtor_refined	0.346
r_symmetry_hbond_refined	0.315
r_symmetry_vdw_refined	0.305
r_nbd_refined	0.284
r_xyhbond_nbd_refined	0.184
r_chiral_restr	0.094
r_bond_refined_d	0.012
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3721
Nucleic Acid Atoms
Solvent Atoms	20
Heterogen Atoms

Software

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

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.