Experiment: 5DUD

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3MML

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	Reservoir solution: 0.1 M Bicine, pH 8.5, 20% PEG 6000. Protein storage buffer: 20 mM Tris-pH 8.0, 300 mM NaCl, 10% glycerol. Additives: TCEP, malonamide.

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.11	α = 90
b = 88.78	β = 101.91
c = 83.7	γ = 90

Symmetry
Space Group	P 1 21 1

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	ADSC QUANTUM 315r		2008-04-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	1.0	ALS	8.2.1

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	2.8	15	98.9	0.08	14.43	3.67		23159			71.04

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.88	97.4		0.478	0.557	2.66	3.77

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	3MML	2.8	15	22991	1185	98.62	0.2685	0.2675	0.29	0.2876	0.31	RANDOM	48.44

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]
2.078		-3.5418	3.2709		-5.3489

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	3.27
t_omega_torsion	2.51
t_angle_deg	0.95
t_bond_d	0.008
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	3.27
t_omega_torsion	2.51
t_angle_deg	0.95
t_bond_d	0.008
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14165
Nucleic Acid Atoms
Solvent Atoms	166
Heterogen Atoms

Software

Software
Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
MR-Rosetta	phasing
PDB_EXTRACT	data extraction

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.