2NU4 | pdb_00002nu4

Accommodation of positively-charged residues in a hydrophobic specificity pocket: Crystal structures of SGPB in complex with OMTKY3 variants Lys18I and Arg18I

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3SGB	PDB ENTRY 3SGB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	PEG 4000, SODIUM POTASSIUM PHOSPHATE at pH 7.1 24h before data collection, crystal was transferred to PEG4000, NaKHPO4 at pH 10.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.452	α = 90
b = 54.689	β = 119.33
c = 45.633	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	IMAGE PLATE	MAC Science DIP-2030	mirrors	1998-03-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.75	20	95.9	0.173	8.59	3.6	19840	19056		5

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)
	1.75	1.76	70.4		0.359	1.72

Refinement

Statistics
Diffraction ID	Structure Solution 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)	Mean Isotropic B
X-RAY DIFFRACTION	MIR	PDB ENTRY 3SGB	1.75	20	19056		95.9	0.17	0.17	0.16

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]

RMS Deviations
Key	Refinement Restraint Deviation
t_dihedral_angle_d	16.273
t_angle_deg	1.016
t_bond_d	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1717
Nucleic Acid Atoms
Solvent Atoms	174
Heterogen Atoms

Software

Software
Software Name	Purpose
DIP	data collection
X-PLOR	model building
TNT	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	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.