Experiment: 7Z5I

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	295	PME 3350, 2% MPD, 0.05M Sodium Acetate, pH 4.5

Crystal Properties
Matthews coefficient	Solvent content
3.09	60.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 166.7	α = 90
b = 33.923	β = 91.04
c = 53.729	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	PIXEL	DECTRIS PILATUS 6M		2018-04-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.972	ESRF	ID23-1

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	2.996	83.336	91.3	0.067	0.083	0.047	6.9	2.8	5721	5721

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.16	92		0.912	0.912	1.119	0.638	0.8	2.7

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	1MDY	3	53.34	5157	560	90.5	0.2332	0.2272	0.2876	RANDOM	99.019

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]
10.36		-8.35	-3.56		-6.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.402
r_dihedral_angle_3_deg	24.741
r_dihedral_angle_4_deg	19.762
r_dihedral_angle_1_deg	7.026
r_angle_refined_deg	1.477
r_angle_other_deg	1.471
r_chiral_restr	0.093
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_bond_other_d	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.402
r_dihedral_angle_3_deg	24.741
r_dihedral_angle_4_deg	19.762
r_dihedral_angle_1_deg	7.026
r_angle_refined_deg	1.477
r_angle_other_deg	1.471
r_chiral_restr	0.093
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_bond_other_d	0.004
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	942
Nucleic Acid Atoms	738
Solvent Atoms	3
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
PDB_EXTRACT	data extraction
XDS	data scaling
PHASER	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 R01GM133198.