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)
TypeSourceAccession CodeDetails
experimental modelPDB 1U1BPDB ENTRY 1U1B

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
172980.1 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 coefficientSolvent content
2.0239.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 30.73α = 90
b = 74.85β = 107.8
c = 50.52γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVOSMIC MIRRORS2007-04-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.629.5491.20.02716.82.612590033.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6664.20.342.42.15

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1U1B1.629.5425900233602540900.2030.1970.253RANDOM38.71
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]
2.850.94-1.64-0.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.458
r_dihedral_angle_3_deg15.327
r_dihedral_angle_4_deg12.911
r_scangle_it7.017
r_dihedral_angle_1_deg6.662
r_scbond_it5.312
r_mcangle_it4.409
r_mcbond_it3.43
r_angle_refined_deg1.549
r_mcbond_other0.925
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.458
r_dihedral_angle_3_deg15.327
r_dihedral_angle_4_deg12.911
r_scangle_it7.017
r_dihedral_angle_1_deg6.662
r_scbond_it5.312
r_mcangle_it4.409
r_mcbond_it3.43
r_angle_refined_deg1.549
r_mcbond_other0.925
r_angle_other_deg0.689
r_symmetry_hbond_refined0.234
r_nbd_refined0.22
r_nbd_other0.216
r_xyhbond_nbd_refined0.209
r_symmetry_vdw_other0.201
r_nbtor_refined0.192
r_xyhbond_nbd_other0.165
r_symmetry_vdw_refined0.163
r_nbtor_other0.096
r_chiral_restr0.094
r_symmetry_hbond_other0.091
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms1902
Nucleic Acid Atoms
Solvent Atoms211
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling