6TSC | pdb_00006tsc

OphMA I407P complex with SAH

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5N0O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		289	0.3-0.4 M KSCN, 0.1 M Bicine pH 8-9, 1.8-2.5 M sodium malonate

Crystal Properties
Matthews coefficient	Solvent content
3.86	68.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.379	α = 90
b = 89.379	β = 90
c = 157.001	γ = 120

Symmetry
Space Group	P 32 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		2019-05-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	2.19	52.33	100	0.058	1	15.7	11.1		38116

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.19	2.23	99.7		2.088	0.9	1.1	10.9

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	5N0O	2.19	52.33	36209	1846	99.93	0.209	0.2078	0.2137	0.2322	0.2348	RANDOM	99.841

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]
2.87	1.44		2.87		-9.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.789
r_dihedral_angle_4_deg	20.355
r_dihedral_angle_3_deg	15.709
r_dihedral_angle_1_deg	6.939
r_angle_refined_deg	1.518
r_angle_other_deg	1.192
r_chiral_restr	0.063
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2960
Nucleic Acid Atoms
Solvent Atoms	3
Heterogen Atoms	26

Software

Software
Software Name	Purpose
xia2	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
PHASER	phasing