3AHW | pdb_00003ahw

Crystal Structure of Ustilago sphaerogena Ribonuclease U2 complexed with adenosine 2'-monophosphate

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	hanging drop, vapor diffusion	6.5	293	PEG 8000, pH 6.5, hanging drop, vapor diffusion, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.994	α = 90
b = 35.94	β = 103.42
c = 36.151	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	CCD	ADSC QUANTUM 4r		2010-01-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-6A	0.978	Photon Factory	BL-6A

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	1.03	37.9	99.2	0.093	36.2	6.5	48243	47871			11.07

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)
	1.03	1.057	93.9		0.395	2.2	3	3554

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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 3AGN	1.03	25.14	47871	2445	99.23	0.137	0.137	0.14	0.144	0.15	RANDOM	10.729

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]
0.06		0.21	-0.01		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.075
r_dihedral_angle_3_deg	11.009
r_dihedral_angle_4_deg	7.816
r_dihedral_angle_1_deg	7.202
r_scangle_it	4.455
r_scbond_it	3.031
r_mcangle_it	2.269
r_angle_refined_deg	1.656
r_mcbond_it	1.5
r_rigid_bond_restr	1.155

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.075
r_dihedral_angle_3_deg	11.009
r_dihedral_angle_4_deg	7.816
r_dihedral_angle_1_deg	7.202
r_scangle_it	4.455
r_scbond_it	3.031
r_mcangle_it	2.269
r_angle_refined_deg	1.656
r_mcbond_it	1.5
r_rigid_bond_restr	1.155
r_angle_other_deg	0.927
r_mcbond_other	0.461
r_chiral_restr	0.093
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_bond_other_d	0.008
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	870
Nucleic Acid Atoms
Solvent Atoms	156
Heterogen Atoms	27

Software

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

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.