1MGW | pdb_00001mgw

Crystal structure of RNase Sa3, cytotoxic microbial ribonuclease

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.6	293	Tris, HCl, HEPES, lithium sulphate, pH 7.6, VAPOR DIFFUSION, HANGING DROP at 293K

Crystal Properties
Matthews coefficient	Solvent content
3.8	68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.72	α = 90
b = 64.72	β = 90
c = 69.57	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MARRESEARCH		2000-04-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X31	1.100	EMBL/DESY, HAMBURG	X31

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	2	29.6	100	0.06	31.6	9.5	11799	11799			28.5

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)
	2	2.02	99.5		0.306	5.8	7.9	390

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1RGG	2	29	11799	11760	559	100	0.155	0.155	0.154	0.168	0.212	RANDOM	25.813

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]
2.09	1.05		2.09		-3.14

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	14.373
p_scangle_it	5.842
r_scangle_it	5.842
r_dihedral_angle_1_deg	5.479
r_sphericity_bonded	4.616
p_scbond_it	3.836
r_scbond_it	3.836
p_mcangle_it	2.56
r_mcangle_it	2.56
r_rigid_bond_restr	1.954
p_angle_deg	1.831
p_angle_d	1.831
r_angle_refined_deg	1.831
p_mcbond_it	1.642
r_mcbond_it	1.642
r_angle_other_deg	0.824
p_hb_or_metal_coord	0.171
p_chiral_restr	0.105
r_chiral_restr	0.105
p_bond_d	0.021
r_bond_refined_d	0.021
p_plane_restr	0.008
r_gen_planes_refined	0.008
r_gen_planes_other	0.003
r_bond_other_d	0.001
p_planar_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	782
Nucleic Acid Atoms
Solvent Atoms	145
Heterogen Atoms	1

Software

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