6SJJ | pdb_00006sjj

A new modulated crystal structure of ANS complex of St John's wort Hyp-1 protein with 36 protein molecules in the asymmetric unit of the supercell

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4N3E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		292	0.1 M HEPES buffer pH 7.5, 1.3 M sodium citrate precipitant pH 6.3, 1:1 protein:reservoir volume ratio

Crystal Properties
Matthews coefficient	Solvent content
3.16	61.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 145.85	α = 90
b = 145.85	β = 90
c = 385.4	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 2M		2014-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.918	BESSY	14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.3	31.58	99.28	0.066	0.978	6.22	7.2		127324			67.46

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.39			0.691	0.62

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	FREE R-VALUE	4N3E	2.3	31.58	123350	3974	99.28	0.2264	0.226	0.27	0.2548	0.28	RANDOM	67.461

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]
-26.22		-10.81	6.51		19.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.3
r_dihedral_angle_4_deg	16.525
r_dihedral_angle_3_deg	15.806
r_dihedral_angle_1_deg	4.542
r_angle_refined_deg	1.837
r_angle_other_deg	1.086
r_chiral_restr	0.083
r_gen_planes_other	0.014
r_gen_planes_refined	0.011
r_bond_refined_d	0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.3
r_dihedral_angle_4_deg	16.525
r_dihedral_angle_3_deg	15.806
r_dihedral_angle_1_deg	4.542
r_angle_refined_deg	1.837
r_angle_other_deg	1.086
r_chiral_restr	0.083
r_gen_planes_other	0.014
r_gen_planes_refined	0.011
r_bond_refined_d	0.01
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	44726
Nucleic Acid Atoms
Solvent Atoms	152
Heterogen Atoms	3465

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	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 R01GM157729.