Experiment: 5EZR

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5DYL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	293	15.5% Peg3350, 0.1M Hepes pH 7, 0.1M Succinate pH 7

Crystal Properties
Matthews coefficient	Solvent content
3.96	68.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 191.103	α = 90
b = 117.967	β = 95.17
c = 68.162	γ = 90

Symmetry
Space Group	C 1 2 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		2015-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97929	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.5	50	97.7	0.075	0.086	0.042	7.6	4.1		50530

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.54	81.9		0.678	0.78	0.38	0.821		3.9	2107

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5DYL	2.5	50	48165	2360	97.39	0.2271	0.2252	0.2657	RANDOM	80.716

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]
10.49		-1.7	-3.48		-6.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.049
r_dihedral_angle_4_deg	16.195
r_dihedral_angle_3_deg	14.215
r_mcangle_it	5.682
r_dihedral_angle_1_deg	5.622
r_mcbond_it	3.432
r_mcbond_other	3.432
r_angle_refined_deg	1.196
r_angle_other_deg	0.906
r_chiral_restr	0.068

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.049
r_dihedral_angle_4_deg	16.195
r_dihedral_angle_3_deg	14.215
r_mcangle_it	5.682
r_dihedral_angle_1_deg	5.622
r_mcbond_it	3.432
r_mcbond_other	3.432
r_angle_refined_deg	1.196
r_angle_other_deg	0.906
r_chiral_restr	0.068
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6187
Nucleic Acid Atoms
Solvent Atoms	69
Heterogen Atoms	38

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
REFMAC	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.