3N2D | pdb_00003n2d

Crystal Structure of the Complex of type I Ribosome inactivating protein with hexapeptide Ser-Asp-Asp-Asp-Met-Gly at 2.2 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.7	298	14% PEG 6000, 0.1M Sodium Phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.186	α = 90
b = 131.186	β = 90
c = 40.734	γ = 120

Symmetry
Space Group	H 3

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	MARRESEARCH	Mirror	2009-05-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5414

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.22	65.7	99.2	0.056	12.6		12968	12968			42.124

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.22	2.29	96.2		0.315	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1AHA	2.22	19.84	12968	12264	627	99.44	0.18626	0.18608	0.18292	0.19	0.2219	0.24	RANDOM	42.229

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]
-1.41	-0.7		-1.41		2.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.233
r_dihedral_angle_4_deg	25.32
r_dihedral_angle_3_deg	17.209
r_dihedral_angle_1_deg	5.367
r_scangle_it	3.37
r_scbond_it	2.148
r_angle_refined_deg	1.534
r_mcangle_it	1.351
r_mcbond_it	0.822
r_nbtor_refined	0.309
r_symmetry_hbond_refined	0.26
r_nbd_refined	0.217
r_symmetry_vdw_refined	0.208
r_xyhbond_nbd_refined	0.19
r_chiral_restr	0.111
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1954
Nucleic Acid Atoms
Solvent Atoms	189
Heterogen Atoms	28

Software

Software
Software Name	Purpose
DENZO	data reduction
AMoRE	phasing
REFMAC	refinement
AUTOMAR	data reduction
SCALEPACK	data scaling