2OQA | pdb_00002oqa

X-ray Sequence and Crystal Structure of Luffaculin 1, a Novel Type 1 Ribosome-inactivating Protein

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	Other		a homology model built based on the sequence luffin a

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	298	28% (w/v) PEG 6000, 0.1M citrate buffer(containing 0.02% (w/v) sodium azide)', pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.135	α = 89.07
b = 46.813	β = 80.01
c = 83.571	γ = 72.14

Symmetry
Space Group	P 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	CCD	MAR CCD 130 mm	mirrors	2005-05-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.05	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.4	33.9	86.7	0.03	0.115	21.8	1.9		94795	2	2	18.964

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.436	62		0.03	0.115	4.6	1.7	94795

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	a homology model built based on the sequence luffin a	1.4	33.9	2	2	94795	4750	86.7	0.21405	0.21313	0.21313	0.2149	0.23157	RANDOM	18.964

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]
-0.69	-0.42	0.46	1.67	-1.05	-0.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.287
r_dihedral_angle_4_deg	20.006
r_dihedral_angle_3_deg	11.308
r_dihedral_angle_1_deg	4.628
r_scangle_it	2.346
r_scbond_it	1.554
r_angle_refined_deg	1.153
r_mcangle_it	0.965
r_mcbond_it	0.577
r_nbtor_refined	0.307

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.287
r_dihedral_angle_4_deg	20.006
r_dihedral_angle_3_deg	11.308
r_dihedral_angle_1_deg	4.628
r_scangle_it	2.346
r_scbond_it	1.554
r_angle_refined_deg	1.153
r_mcangle_it	0.965
r_mcbond_it	0.577
r_nbtor_refined	0.307
r_nbd_refined	0.214
r_symmetry_vdw_refined	0.153
r_xyhbond_nbd_refined	0.133
r_symmetry_hbond_refined	0.101
r_chiral_restr	0.077
r_bond_refined_d	0.007
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3600
Nucleic Acid Atoms
Solvent Atoms	490
Heterogen Atoms	87

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	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.