3BWH | pdb_00003bwh

Atomic resolution structure of cucurmosin, a novel type 1 RIP from the sarcocarp of Cucurbita moschata

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.9	298	100 mM phosphate buffer, 20% PEG6000, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 5.90

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.763	α = 90
b = 58.782	β = 90
c = 99.523	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	CCD	MARMOSAIC 325 mm CCD	MIRRORS	2002-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID		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	50	84	0.108	0.108	22.9	7.4		111623			9.7

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	1.04	40.6		0.393	0.393	1.3	2.1

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1TCS	1	38.52	105926	105926	5611	84	0.172	0.171	0.18	0.179	RANDOM	9.72

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]
-0.06			0.1		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.425
r_dihedral_angle_4_deg	17.94
r_dihedral_angle_3_deg	9.785
r_dihedral_angle_1_deg	5.465
r_sphericity_free	2.944
r_scangle_it	2.448
r_sphericity_bonded	2.1
r_scbond_it	1.863
r_angle_refined_deg	1.498
r_angle_other_deg	1.476
r_mcangle_it	1.345
r_mcbond_it	1.084
r_rigid_bond_restr	1.074
r_mcbond_other	0.376
r_nbd_refined	0.212
r_symmetry_vdw_refined	0.209
r_symmetry_vdw_other	0.193
r_nbd_other	0.176
r_nbtor_refined	0.171
r_symmetry_hbond_refined	0.155
r_chiral_restr	0.121
r_xyhbond_nbd_refined	0.112
r_nbtor_other	0.085
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1907
Nucleic Acid Atoms
Solvent Atoms	255
Heterogen Atoms	95

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing