Experiment: 7LVY

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6PNT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	295	2.1 M DL-Malic acid

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.159	α = 90
b = 61.596	β = 106.15
c = 78.861	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 EIGER X 16M		2020-08-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0000	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.85	40	96.2	0.058	0.058	0.069	0.037	0.997	23.1	3.5		41813		-3

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)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.88	96.8		0.479	0.479	0.573	0.309	0.867	2.1	3.1

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	6PNT	1.85	38.88	39812	2001	95.96	0.1835	0.1818	0.19	0.2189	0.23	RANDOM	32.675

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]
3.82		-1.31	-1.18		-1.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.34
r_dihedral_angle_4_deg	17.007
r_dihedral_angle_3_deg	13.16
r_dihedral_angle_1_deg	6.001
r_angle_other_deg	2.275
r_angle_refined_deg	1.684
r_chiral_restr	0.087
r_bond_other_d	0.034
r_bond_refined_d	0.012
r_gen_planes_other	0.012

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.34
r_dihedral_angle_4_deg	17.007
r_dihedral_angle_3_deg	13.16
r_dihedral_angle_1_deg	6.001
r_angle_other_deg	2.275
r_angle_refined_deg	1.684
r_chiral_restr	0.087
r_bond_other_d	0.034
r_bond_refined_d	0.012
r_gen_planes_other	0.012
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3462
Nucleic Acid Atoms
Solvent Atoms	358
Heterogen Atoms	49

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
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.