3DJO

Bovine Seminal Ribonuclease uridine 2' phosphate complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1R5DPDB ENTRY 1R5D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.528930% PEG4000, 0.1M sodium acetate, 0.1M Tris/HCl, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.1643.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.311α = 90
b = 59.067β = 90
c = 82.495γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2007-02-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.8088EMBL/DESY, HAMBURGX13

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.627.799.90.06612.45.93187131815-315.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6398.40.46634.19056

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1R5D1.627.730202160599.830.186280.184140.22638RANDOM
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.296
r_dihedral_angle_4_deg15.447
r_dihedral_angle_3_deg11.936
r_dihedral_angle_1_deg5.517
r_angle_refined_deg1.171
r_nbtor_refined0.291
r_nbd_refined0.192
r_symmetry_vdw_refined0.168
r_symmetry_hbond_refined0.137
r_xyhbond_nbd_refined0.121
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.296
r_dihedral_angle_4_deg15.447
r_dihedral_angle_3_deg11.936
r_dihedral_angle_1_deg5.517
r_angle_refined_deg1.171
r_nbtor_refined0.291
r_nbd_refined0.192
r_symmetry_vdw_refined0.168
r_symmetry_hbond_refined0.137
r_xyhbond_nbd_refined0.121
r_bond_refined_d0.008
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1882
Nucleic Acid Atoms
Solvent Atoms327
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing