Experiment: 3MDT

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Q9F	PDB ENTRY 2Q9F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.8	291	8% PEG 8000, 20% glycerol, 50 mM KPi, 0.03% undecylmaltoside, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.6	α = 90
b = 121.6	β = 90
c = 143.83	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	ADSC QUANTUM 315r	Rh coated flat mirror	2009-07-31		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	0.979	SSRL	BL7-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.3	92.86	99	0.065	0.065	5	3.6	45803	45803			48.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.42	99		0.392	0.392	1.9	3.5	6719

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2Q9F	2.3	92.86	45787	43462	2325	98.86	0.232	0.232	0.229	0.287	RANDOM	35.1

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]
-1.05			-1.05		2.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.032
r_dihedral_angle_3_deg	15.494
r_dihedral_angle_4_deg	10.488
r_dihedral_angle_1_deg	4.306
r_angle_refined_deg	0.854
r_scangle_it	0.716
r_scbond_it	0.418
r_mcangle_it	0.38
r_mcbond_it	0.207
r_chiral_restr	0.068

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.032
r_dihedral_angle_3_deg	15.494
r_dihedral_angle_4_deg	10.488
r_dihedral_angle_1_deg	4.306
r_angle_refined_deg	0.854
r_scangle_it	0.716
r_scbond_it	0.418
r_mcangle_it	0.38
r_mcbond_it	0.207
r_chiral_restr	0.068
r_bond_refined_d	0.006
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6836
Nucleic Acid Atoms
Solvent Atoms	378
Heterogen Atoms	136

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
MOSFLM	data reduction
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.