Experiment: 5EQM

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4O4T

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	1.6 M ammonium sulfate, 0.1 M MES, 10 % dioxane

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.372	α = 90
b = 87.372	β = 90
c = 113.284	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	293	CCD	MAR CCD 165 mm		2012-05-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE CRISTAL	0.4540	SOLEIL	CRISTAL

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	2.05	45.345	97.6	0.112	0.126	0.057	9.8	5	10340	10340

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.16	97.8		0.541	0.541	0.268	1.3	5	1509

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	4O4T	2.05	20	9463	477	93.13	0.1746	0.1716	0.18	0.2371	0.23	RANDOM	33.088

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]
-0.04	-0.02		-0.04		0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.825
r_dihedral_angle_4_deg	21.628
r_dihedral_angle_3_deg	15.984
r_dihedral_angle_1_deg	6.713
r_mcangle_it	5.709
r_mcbond_it	3.93
r_mcbond_other	3.92
r_angle_refined_deg	2.219
r_angle_other_deg	2.014
r_chiral_restr	0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.825
r_dihedral_angle_4_deg	21.628
r_dihedral_angle_3_deg	15.984
r_dihedral_angle_1_deg	6.713
r_mcangle_it	5.709
r_mcbond_it	3.93
r_mcbond_other	3.92
r_angle_refined_deg	2.219
r_angle_other_deg	2.014
r_chiral_restr	0.17
r_bond_refined_d	0.023
r_gen_planes_refined	0.012
r_gen_planes_other	0.005
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1172
Nucleic Acid Atoms
Solvent Atoms	71
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PHASER	phasing
DM	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

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.