3S9Q | pdb_00003s9q

Crystal structure of native type 1 ribosome inactivating protein from Momordica balsamina at 1.67 A resolution

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.7	298	14% PEG6000, 0.1M Sodium Phosphate , pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.181	α = 90
b = 130.181	β = 90
c = 40.292	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	mirrir	2009-07-23	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 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	1.67	65.09	96.2	0.107	15.2		26840	26840			16.7

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)
1	1.67	1.7	82.3		0.433	2.2

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	1AHA	1.67	65.09	26840	26840	1439	96.24	0.18268	0.18262	0.18159	0.18	0.20283	0.21	RANDOM	20.417

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]
-0.71	-0.35		-0.71		1.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.646
r_dihedral_angle_4_deg	21.897
r_dihedral_angle_3_deg	11.946
r_dihedral_angle_1_deg	5.24
r_scangle_it	3.956
r_scbond_it	2.573
r_mcangle_it	1.441
r_angle_refined_deg	1.423
r_mcbond_it	0.853
r_chiral_restr	0.094

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.646
r_dihedral_angle_4_deg	21.897
r_dihedral_angle_3_deg	11.946
r_dihedral_angle_1_deg	5.24
r_scangle_it	3.956
r_scbond_it	2.573
r_mcangle_it	1.441
r_angle_refined_deg	1.423
r_mcbond_it	0.853
r_chiral_restr	0.094
r_bond_refined_d	0.015
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1911
Nucleic Acid Atoms
Solvent Atoms	277
Heterogen Atoms	26

Software

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

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.