3JW1

Crystal Structure of Bovine Pancreatic Ribonuclease Complexed with Uridine-5'-monophosphate at 1.60 A Resolution

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1U1B	PDB ENTRY 1U1B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7	298	0.1 M HEPES BUFFER; Reservoir of 25% PEG3350 in water; droplets were 5-10 mM in basic fuchsin, tobramycin, uridine-5'-monophosphate and 1 mM in ribonuclease A, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.73	α = 90
b = 74.85	β = 107.8
c = 50.52	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	100	IMAGE PLATE	RIGAKU RAXIS IV	OSMIC MIRRORS	2007-04-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200

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	1.6	29.54	91.2	0.027	16.8	2.61		25900			33.2

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	1.6	1.66	64.2		0.34	2.4	2.15

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1U1B	1.6	29.54	25900	23360	2540	90	0.203	0.197	0.253	RANDOM	38.71

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]
2.85		0.94	-1.64		-0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.458
r_dihedral_angle_3_deg	15.327
r_dihedral_angle_4_deg	12.911
r_scangle_it	7.017
r_dihedral_angle_1_deg	6.662
r_scbond_it	5.312
r_mcangle_it	4.409
r_mcbond_it	3.43
r_angle_refined_deg	1.549
r_mcbond_other	0.925
r_angle_other_deg	0.689
r_symmetry_hbond_refined	0.234
r_nbd_refined	0.22
r_nbd_other	0.216
r_xyhbond_nbd_refined	0.209
r_symmetry_vdw_other	0.201
r_nbtor_refined	0.192
r_xyhbond_nbd_other	0.165
r_symmetry_vdw_refined	0.163
r_nbtor_other	0.096
r_chiral_restr	0.094
r_symmetry_hbond_other	0.091
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_gen_planes_other	0.001
r_bond_other_d
r_metal_ion_refined
r_metal_ion_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1902
Nucleic Acid Atoms
Solvent Atoms	211
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling