Experiment: 5ILR

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	293	100 mM Tris-HCl pH 7.4, 1 mM EDTA, 3.0 M Ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.361	α = 90
b = 30.315	β = 105.21
c = 64.368	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	PIXEL	DECTRIS PILATUS 200K	mirrors	2014-03-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54178

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	1.87	50	99.1	0.046	0.053	0.027	11.6	3.7		10786

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	1.87	1.9	98.2		0.216		3

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	2MBW	1.87	33.16	10255	519	98.92	0.166	0.1637	0.2146	RANDOM	20.368

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		-0.65	0.09		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.494
r_dihedral_angle_4_deg	31.449
r_dihedral_angle_3_deg	15.712
r_sphericity_bonded	6.895
r_dihedral_angle_1_deg	5.277
r_mcangle_it	2.478
r_angle_refined_deg	2.03
r_mcbond_it	1.807
r_mcbond_other	1.736
r_angle_other_deg	1.107

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.494
r_dihedral_angle_4_deg	31.449
r_dihedral_angle_3_deg	15.712
r_sphericity_bonded	6.895
r_dihedral_angle_1_deg	5.277
r_mcangle_it	2.478
r_angle_refined_deg	2.03
r_mcbond_it	1.807
r_mcbond_other	1.736
r_angle_other_deg	1.107
r_chiral_restr	0.129
r_bond_refined_d	0.02
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	1202
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms	71

Software

Software
Software Name	Purpose
HKL-3000	phasing
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	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.