Experiment: 3L4M

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MDA	1mda, 1iqc
experimental model	PDB	1IQC	1mda, 1iqc

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.4	293	0.1M MES pH 6.4, 0.1M sodium acetate, 24-30 % w/v PEG 8000, vapor diffusion, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.527	α = 109.94
b = 83.524	β = 91.54
c = 107.782	γ = 105.78

Symmetry
Space Group	P 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	MARMOSAIC 300 mm CCD	BIOMORPH MIRRORS (KIRKPATRICK-BAEZ CONFIGURATION)	2008-11-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.02665	APS	23-ID-B

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	2.01	50	93.1	0.067	0.067	10.74	2.3	113264	105427		-3	27.03

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	2.01	2.08	68.6		0.176	4.3	1.7	11318

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	1mda, 1iqc	2.02	44.49	113788	105423	5298	92.65	0.138	0.138	0.135	0.14	0.189	0.2	RANDOM	15.169

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]
0.01			0.01	-0.01	-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.176
r_dihedral_angle_4_deg	19.323
r_dihedral_angle_3_deg	15.336
r_dihedral_angle_1_deg	6.48
r_scangle_it	5.009
r_scbond_it	3.23
r_angle_refined_deg	2.02
r_mcangle_it	1.922
r_mcbond_it	1.104
r_chiral_restr	0.178

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.176
r_dihedral_angle_4_deg	19.323
r_dihedral_angle_3_deg	15.336
r_dihedral_angle_1_deg	6.48
r_scangle_it	5.009
r_scbond_it	3.23
r_angle_refined_deg	2.02
r_mcangle_it	1.922
r_mcbond_it	1.104
r_chiral_restr	0.178
r_bond_refined_d	0.023
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13231
Nucleic Acid Atoms
Solvent Atoms	1304
Heterogen Atoms	207

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	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.