4Q9F | pdb_00004q9f

Crystal structure of type 1 ribosome inactivating protein from Momordica balsamina in complex with guanosine mono phosphate at 1.75 Angstrom resolution

X-RAY DIFFRACTION

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Starting Model(s)

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

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
2.4	48.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.072	α = 90
b = 130.072	β = 90
c = 39.877	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	MARMOSAIC 225 mm CCD	Mirror	2014-04-07	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	1.75	65.04	100	0.039	41.75	4.8	25324	25324

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	1.75	1.78	99.7		0.554	2.4	4.5

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 (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 3S9Q	1.75	65.04	25324	24033	1291	99.9	0.16702	0.16449	0.17	0.21383	0.22	RANDOM	34.461

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]
-1.28	-0.64		-1.28		4.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.491
r_dihedral_angle_4_deg	21.287
r_dihedral_angle_3_deg	11.663
r_long_range_B_refined	8.085
r_long_range_B_other	8.085
r_scangle_other	5.894
r_dihedral_angle_1_deg	5.348
r_mcangle_it	4.026
r_mcangle_other	4.011
r_scbond_other	3.883
r_scbond_it	3.862
r_angle_other_deg	3.605
r_mcbond_it	2.819
r_mcbond_other	2.814
r_angle_refined_deg	1.834
r_chiral_restr	0.1
r_gen_planes_other	0.015
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_bond_other_d
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1911
Nucleic Acid Atoms
Solvent Atoms	257
Heterogen Atoms	44

Software

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