3D5G | pdb_00003d5g

Structure of ribonuclease Sa2 complexes with mononucleotides: new aspects of catalytic reaction and substrate recognition

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	298	30% ammonium sulphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.94	58.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.655	α = 90
b = 67.667	β = 100.63
c = 57.085	γ = 90

Symmetry
Space Group	C 1 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		2000-09-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X31	1.1	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	1.8	12	97.7	0.037	32.16		34199	34199	2	1	24.34

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)
	1.8	1.82	74.7		0.24

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	1PYL	1.8	11.98	2	32393	32393	1713	97.45	0.1771	0.17366	0.18	0.24323	0.25	RANDOM	22.318

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]
-0.45		0.25	1.46		-0.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.464
r_dihedral_angle_4_deg	19.485
r_dihedral_angle_3_deg	16.117
r_sphericity_free	9.982
r_dihedral_angle_1_deg	7.176
r_scangle_it	4.954
r_sphericity_bonded	4.315
r_scbond_it	3.684
r_mcangle_it	2.739
r_rigid_bond_restr	2.618
r_mcbond_it	2.203
r_angle_refined_deg	1.892
r_angle_other_deg	1.554
r_mcbond_other	0.777
r_symmetry_vdw_refined	0.309
r_xyhbond_nbd_other	0.307
r_symmetry_hbond_refined	0.259
r_symmetry_vdw_other	0.255
r_xyhbond_nbd_refined	0.244
r_nbd_refined	0.231
r_nbd_other	0.231
r_nbtor_refined	0.192
r_chiral_restr	0.112
r_nbtor_other	0.092
r_bond_refined_d	0.022
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001
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	2307
Nucleic Acid Atoms
Solvent Atoms	505
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing