Experiment: 5I48

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1O7J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	285	0.1M HEPES, pH 7.5 and 24% of PEG MME 2000

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.188	α = 90
b = 87.691	β = 90
c = 175.108	γ = 90

Symmetry
Space Group	P 21 21 21

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 225 mm CCD		2015-06-30	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.5	88	95.7	0.051	0.999	23.09	6.97		183230		-3	17.1

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	1.5	1.59	76.2		0.546	3.07

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	1O7J	1.5	87.55	171916	9078	94.48	0.1227	0.1202	0.1706	RANDOM	20.395

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]
-0.75			0.28		0.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.774
r_sphericity_free	25.206
r_dihedral_angle_4_deg	16.852
r_dihedral_angle_3_deg	11.357
r_sphericity_bonded	9.889
r_rigid_bond_restr	8.469
r_dihedral_angle_1_deg	5.612
r_mcangle_it	3.086
r_mcbond_it	2.735
r_mcbond_other	2.735

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.774
r_sphericity_free	25.206
r_dihedral_angle_4_deg	16.852
r_dihedral_angle_3_deg	11.357
r_sphericity_bonded	9.889
r_rigid_bond_restr	8.469
r_dihedral_angle_1_deg	5.612
r_mcangle_it	3.086
r_mcbond_it	2.735
r_mcbond_other	2.735
r_angle_refined_deg	1.961
r_angle_other_deg	1.861
r_chiral_restr	0.131
r_bond_refined_d	0.023
r_bond_other_d	0.014
r_gen_planes_refined	0.013
r_gen_planes_other	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9776
Nucleic Acid Atoms
Solvent Atoms	1004
Heterogen Atoms	36

Software

Software
Software Name	Purpose
XDS	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
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.