Experiment: 9OFT

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1L9V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	100 mM Tris-HCl pH 7.5, 0.2M MgAc, 12% PEG6K

Crystal Properties
Matthews coefficient	Solvent content
3.13	60.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.673	α = 90
b = 108.673	β = 90
c = 153.416	γ = 90

Symmetry
Space Group	I 4 2 2

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 300K	VariMax HF	2024-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.95	35	100	0.172	0.179	0.051	0.997	5.6	12.1		10045

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.95	3.04	100		0.601	0.625	0.17	0.934		13.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.95	34.39	8873	1001	98.18	0.23186	0.2281	0.2364	0.26608	0.2701	RANDOM	47.251

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]
-0.73			-0.73		1.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.968
r_long_range_B_refined	6.82
r_long_range_B_other	6.819
r_dihedral_angle_1_deg	5.584
r_mcangle_it	3.439
r_mcangle_other	3.438
r_scangle_other	3.378
r_mcbond_it	2.036
r_mcbond_other	2.035
r_scbond_it	1.985

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.968
r_long_range_B_refined	6.82
r_long_range_B_other	6.819
r_dihedral_angle_1_deg	5.584
r_mcangle_it	3.439
r_mcangle_other	3.438
r_scangle_other	3.378
r_mcbond_it	2.036
r_mcbond_other	2.035
r_scbond_it	1.985
r_scbond_other	1.985
r_angle_refined_deg	0.822
r_angle_other_deg	0.323
r_chiral_restr	0.04
r_bond_refined_d	0.005
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2546
Nucleic Acid Atoms
Solvent Atoms	7
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
PHENIX	phasing
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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.