4M5A

Crystal structure of the complex of Ribosome inactivating protein from Momordica balsamina inhibited by asymmetric dimethyl arginine at 1.70 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3S9Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	298	14% PEG 6000, 0.1M Sodium Phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.257	α = 90
b = 130.257	β = 90
c = 39.74	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	77	CCD	MARRESEARCH	Mirror	2013-07-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.97	ESRF	BM14

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	1.7	50	100	0.069	23		26101	26101

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	1.7	1.79	99.9		0.596	5

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3S9Q	1.7	37.51	26101	26101	1384	99.39	0.20808	0.20808	0.20146	0.24084	RANDOM	28.212

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]
-0.55	-0.55		-0.55		1.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.787
r_dihedral_angle_4_deg	16.656
r_dihedral_angle_3_deg	14.941
r_dihedral_angle_1_deg	5.366
r_long_range_B_refined	4.997
r_long_range_B_other	4.749
r_scangle_other	1.982
r_mcangle_it	1.897
r_mcangle_other	1.897
r_angle_refined_deg	1.211
r_scbond_it	1.154
r_scbond_other	1.153
r_mcbond_other	1.07
r_mcbond_it	1.069
r_angle_other_deg	0.813
r_chiral_restr	0.063
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1911
Nucleic Acid Atoms
Solvent Atoms	233
Heterogen Atoms	28

Software

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